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Title
Computational Structural Biology Lab
Category
general
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c07f0fe320b7417cb88a7ebe8828aec2
Source URL
http://www.csb.iitkgp.ac.in/applications/PRDBv2.php
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http://www.csb.iitkgp.ac.in/
Crawl Time
2026-03-18T08:15:08+00:00
Rendered Raw Markdown 
# Computational Structural Biology Lab

**Source**: http://www.csb.iitkgp.ac.in/applications/PRDBv2.php
**Parent**: http://www.csb.iitkgp.ac.in/

### Department of Biotechnology Indian Institute of Technology Kharagpur

- [Home](http://www.csb.iitkgp.ac.in/)
- [Research](http://www.csb.iitkgp.ac.in/pages/research.php)
- [Publications](http://www.csb.iitkgp.ac.in/pages/publications.php)
- [Teaching](http://www.csb.iitkgp.ac.in/pages/teaching.php)
- Tutorials
  - [Python Tutorial](http://www.csb.iitkgp.ac.in/tutorials/python/python_index.php)
  - [Gromacs Tutorial](http://www.csb.iitkgp.ac.in/tutorials/gromacs/gromacs_index.php)
- Tools
  - [PRince](http://www.facweb.iitkgp.ac.in/~rbahadur/prince/home.html)
  - [Layers](http://www.csb.iitkgp.ac.in/applications/mol_layers/main)
  - [HotSPRing](http://www.csb.iitkgp.ac.in/applications/HotSPRing/main)
  - [B-Cell epitope prediction](http://www.csb.iitkgp.ac.in/applications/b_cell_epitope_pred/main)
  - [NCodR](http://www.csb.iitkgp.ac.in/applications/NCodR/index)
  - [Nucpred](http://www.csb.iitkgp.ac.in/applications/Nucpred/index)
  - [Rotamers for RBPs](http://www.csb.iitkgp.ac.in/applications/RBP-Rotamer/rotamer)
- Databases
  - [Protein folding similarity](#)
- Benchmarks
  - [Protein-RNA Docking Benchmark version 3](http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php)
  - [Protein-RNA Docking Benchmark version 2](http://www.csb.iitkgp.ac.in/applications/PRDBv2.php)
  - [Protein-RNA Docking Benchmark version 1](http://www.csb.iitkgp.ac.in/applications/benchmark.php)
  - [Protein-RNA Affinity Benchmark](http://www.csb.iitkgp.ac.in/applications/affinity.php)
  - [ProRBR Dataset](http://www.csb.iitkgp.ac.in/applications/proRBR_dataset/proRBR)
- [Members](http://www.csb.iitkgp.ac.in/pages/members.php)
- Links
  - [Bioinformatics Centre](http://www.csb.iitkgp.ac.in/bioinformatics_centre/index.html)
  - [Homepage IITKGP](http://www.iitkgp.ac.in)
  - [Homepage Department of Biotechnology](http://www.bt.iitkgp.ac.in)
- [Contact](http://www.csb.iitkgp.ac.in/pages/contact.php)

**Supplementary Information for [Protein
RNA docking benchmark Version 2](http://onlinelibrary.wiley.com/doi/10.1002/prot.25211/full)**

Each folder
contains the protein-RNA complex, the unbound structure of protein and/or RNA
(wherever available) along with the transformed coordinates of unbound protein
and/or RNA subunits superposed with the bound subunits. The subunits have been
filtered and only chains of interest are retained in the PDB files.

[Click
here](http://www.csb.iitkgp.ac.in/static/images/labMembers/6 Alumni/0Nithin C.pdf/PRDBv2.0.zip) to download the protein-RNA docking benchmark dataset. (Description of
the dataset can be found [here](http://www.csb.iitkgp.ac.in/static/images/labMembers/6 Alumni/0Nithin C.pdf/PRDBv2.0_Description.php).)

# Table 1: The benchmark dataset of protein-RNA complexes.

|  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| **Bounda** | | | **Unbound (PDB id)a** | | **Bb** | **rmsd** | | | | | **fnat** | **GDT\_TS** | **LGA\_S** | **Category** |
| **PDB id** | **Protein** | **RNA** | **Protein** | **RNA** |  | **c-rmsdc** | **p-rmsdd** | **i-rmsde** | | |
|  |  |  |  |  |  | **Cα** | **P** | **Cα+P** |  |
| **I. Unbound-Unbound cases (21)** | | | | | | | | | | | | | | |
| **(A) Complexes with tRNA (10)** | | | | | | | | | | | | | | |
| [1ASY](http://www.rcsb.org/pdb/explore/explore.do?structureId=1asy) (A:R) | ‎*S. cerevisiae* aspartyl-tRNA synthetase | tRNA-Asp | [1EOV](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EOV) (A) | [2TRA](http://www.rcsb.org/pdb/explore/explore.do?structureId=2TRA) (A) | 4430 | 1.5 | 4.9 | 1.3 | 3.3 | 2.3 | 34.0 | 85.4 | 92.8 | R |
| [1B23](http://www.rcsb.org/pdb/explore/explore.do?structureId=1B23) (P:R) | *T. aquaticus* EF-TU | *E. coli* tRNA-Cys | [1TUI](http://www.rcsb.org/pdb/explore/explore.do?structureId=1TUI) (A) | [1U0B](http://www.rcsb.org/pdb/explore/explore.do?structureId=1U0B)\* (A) | 2616 | 10.0 | 7.2 | 13.3 | 13.0 | 13.2 | 19.0 | 50.3 | 47.7 | X |
| [1C0A](http://www.rcsb.org/pdb/explore/explore.do?structureId=1C0A) (A:B) | *E. coli*aspartyl-tRNA synthetase | tRNA-Asp | [1EQR](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EQR) (A) | [1EFW](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EFW)\* (C) | 4504 | 1.6 | 1.8 | 1.6 | 1.8 | 1.7 | 70.8 | 84.0 | 92.0 | S |
| [1QTQ](http://www.rcsb.org/pdb/explore/explore.do?structureId=1QTQ) (A:B) | *E. coli* glutaminyl-tRNA synthetase | tRNA-Gln | [1NYL](http://www.rcsb.org/pdb/explore/explore.do?structureId=1NYL) (A) | [3KNH](http://www.rcsb.org/pdb/explore/explore.do?structureId=3KNH)\* (Y) | 5202 | 1.6 | 4.8 | 1.8 | 6.4 | 4.0 | 41.3 | 86.7 | 93.0 | S |
| [2BTE](http://www.rcsb.org/pdb/explore/explore.do?structureId=2BTE) (A:B) | *T. thermophilus* leucyl-tRNA synthetase | tRNA-Leu | [1OBC](http://www.rcsb.org/pdb/explore/explore.do?structureId=1OBC) (A) | [2NQP](http://www.rcsb.org/pdb/explore/explore.do?structureId=2NQP)\* (F) | 3430 | 1.2 | 4.6 | 1.3 | 4.1 | 2.5 | 46.2 | 77.1 | 68.4 | R |
| [2DRB](http://www.rcsb.org/pdb/explore/explore.do?structureId=2DRB) (A:B) | *A. fulgidus* CCA-adding enzyme | tRNAminiCCA | [1UET](http://www.rcsb.org/pdb/explore/explore.do?structureId=1UET) (A) | [3Q1Q](http://www.rcsb.org/pdb/explore/explore.do?structureId=3Q1Q)\* (C) | 3198 | 1.1 | 3.4 | 1.8 | 4.2 | 2.5 | 22.0 | 86.8 | 87.8 | S |
| [2FMT](http://www.rcsb.org/pdb/explore/explore.do?structureId=2FMT) (A:C) | *E. coli* methionyl-tRNAfmet transformylase | tRNAfmet | [1FMT](http://www.rcsb.org/pdb/explore/explore.do?structureId=1FMT) (A) | [3CW6](http://www.rcsb.org/pdb/explore/explore.do?structureId=3CW6) (A) | 2940 | 1.2 | 2.3 | 0.9 | 2.5 | 1.7 | 44.8 | 91.2 | 96.1 | R |
| [2ZZM](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZZM) (A:B) | *M. jannaschii* tRNA (guanine(37)-N1)-methyltransferase Trm5b | tRNA-Leu | [2YX1](http://www.rcsb.org/pdb/explore/explore.do?structureId=2YX1) (A) | [1WZ2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WZ2)\* (C) | 4523 | 15.1 | 4.6 | 20.0 | 6.4 | 12.9 | 43.6 | 74.5 | 73.9 | X |
| [3HL2](http://www.rcsb.org/pdb/explore/explore.do?structureId=3HL2) (AA'BB':E) | *H. sapiens* selenium transferase | tRNA-Sec | [3BC8](http://www.rcsb.org/pdb/explore/explore.do?structureId=3BC8) (AA'A''A''') | [3RG5](http://www.rcsb.org/pdb/explore/explore.do?structureId=3RG5) (A) | 2186 | 0.6 | 5.2 | 1.3 | 6.0 | 4.3 | 39.4 | 98.0 | 98.9 | R |
| [3VJR](http://www.rcsb.org/pdb/explore/explore.do?structureId=3VJR) (A:B) | *E. coli* peptidyl-tRNA hydrolase | tRNA CCA-acceptor | [2PTH](http://www.rcsb.org/pdb/explore/explore.do?structureId=2PTH) (A) | [1NJM](http://www.rcsb.org/pdb/explore/explore.do?structureId=1NJM)\* (5) | 1354 | 0.8 | 3.7 | 0.8 | 3.8 | 2.0 | 14.3 | 95.9 | 97.9 | R |
| **(B) Ribosomal proteins (3)** | | | | | | | | | | | | | | |
| [1DFU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1DFU) (P:MN) | *E. coli r*ibosomal protein L25 | 5s rRNA | [**1B75**](http://www.rcsb.org/pdb/explore/explore.do?structureId=1B75) **(A)** | [364D](http://www.rcsb.org/pdb/explore/explore.do?structureId=364D) (CB) | 1690 | 3.0 | 5.3 | 3.0 | 4.4 | 3.7 | 14.3 | 73.4 | 70.4 | X |
| [1FEU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1FEU) (A:BC) | *T. thermophilus* ribosomal protein L5 | 5s rRNA | [2J01](http://www.rcsb.org/pdb/explore/explore.do?structureId=2J01) (Z) | [364D](http://www.rcsb.org/pdb/explore/explore.do?structureId=364D)\* (BC) | 1595 | 2.1 | 3.3 | 2.4 | 2.8 | 2.6 | 55.1 | 82.1 | 80.7 | S |
| [1MMS](http://www.rcsb.org/pdb/explore/explore.do?structureId=1MMS) (A:C) | *T. maritima* ribosomal protein L11 | 23S rRNA fragment | [**2K3F**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2K3F) **(A)** | [3I9C](http://www.rcsb.org/pdb/explore/explore.do?structureId=3I9C)\* (A:1080-1129) | 2455 | 3.5 | 1.6 | 4.1 | 1.6 | 3.3 | 35.6 | 65.2 | 62.3 | X |
| **(C) Duplex RNA (4)** | | | | | | | | | | | | | | |
| [1OOA](http://www.rcsb.org/pdb/explore/explore.do?structureId=1OOA) (A:C) | *M. musculus* NF-kappaB p50 | aptamer RNA | [1LE5](http://www.rcsb.org/pdb/explore/explore.do?structureId=1LE5) (B) | [**2JWV**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JWV)**\* (A)** | **1909** | 6.2 | 6.7 | 5.5 | 7.0 | 6.3 | 50.0 | 64.1 | 62.7 | X |
| [1R3E](http://www.rcsb.org/pdb/explore/explore.do?structureId=1R3E) (A:C) | *T. maritime* pseudouridine synthase TruB | tRNA fragment | [1ZE1](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZE1) (A) | [1EHZ](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EHZ) (A:49-65) | 3680 | 2.0 | 4.9 | 3.3 | 4.9 | 3.6 | 50.0 | 82.9 | 76.4 | X |
| [2R8S](http://www.rcsb.org/pdb/explore/explore.do?structureId=2R8S) (LH:R) | *M. musculus* synthetic FAB | ribozyme | [2HFF](http://www.rcsb.org/pdb/explore/explore.do?structureId=2HFF) (AB) | [1HR2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1HR2) (A) | 2510 | 1.6 | 4.3 | 2.9 | 2.1 | 2.5 | 50.9 | 87.1 | 93.8 | S |
| [3SNP](http://www.rcsb.org/pdb/explore/explore.do?structureId=3SNP) (A:C) | *O. cuniculus* iron regulatory protein 1 | ferritin H IRE RNA | [2B3Y](http://www.rcsb.org/pdb/explore/explore.do?structureId=2B3Y) (A) | [1AQO](http://www.rcsb.org/pdb/explore/explore.do?structureId=1AQO)\* (A) | 2872 | 0.7 | 3.8 | 14.5 | 3.3 | 12.8 | 31.3 | 44.2 | 40.2 | X |
| **(D) Single-stranded RNA (4)** | | | | | | | | | | | | | | |
| [1JBS](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JBS) (A:C) | *A. restrictus* restrictocin | SRD RNA analogue | [1AQZ](http://www.rcsb.org/pdb/explore/explore.do?structureId=1AQZ) (A) | [1Q9A](http://www.rcsb.org/pdb/explore/explore.do?structureId=1Q9A) (A) | 1310 | 0.7 | 3.4 | 0.6 | 3.2 | 1.9 | 62.1 | 97.0 | 98.9 | R |
| [1WSU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WSU) (A:E) | *M. thermoacetica* elongation factor SelB | SECIS RNA | [1LVA](http://www.rcsb.org/pdb/explore/explore.do?structureId=1LVA) (A) | [2RLU](http://www.rcsb.org/pdb/explore/explore.do?structureId=2RLU) (A) | 940 | 0.7 | 4.2 | 0.5 | 1.1 | 0.8 | 73.7 | 98.0 | 98.5 | R |
| [1ZBH](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZBH) (AD:E) | *H. sapiens* exonuclease ERI1 | histone mRNA | [1ZBU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZBU) (AD) | [**1JU7**](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JU7) **(A)** | **1760** | 0.6 | 3.6 | 0.6 | 3.4 | 2.0 | 72.7 | 49.6 | 49.8 | R |
| [2BH2](http://www.rcsb.org/pdb/explore/explore.do?structureId=2BH2) (A:C) | *E. coli* methyltransferase RumA | 23S rRNA | [1UWV](http://www.rcsb.org/pdb/explore/explore.do?structureId=1UWV) (A) | [1JZX](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JZX)\* (A:1915-1951) | 4491 | 1.4 | 9.8 | 0.7 | 10.5 | 6.0 | 30.4 | 86.0 | 93.5 | R |
| **II. Unbound-Bound (95)** | | | | | | | | | | | | | | |
| **(A) Complexes with tRNA (16)** | | | | | | | | | | | | | | |
| [1F7U](http://www.rcsb.org/pdb/explore/explore.do?structureId=1F7U) (A:B) | *S. cerevisiae* arginyl-tRNA synthetase | tRNA-Arg | [1BS2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1BS2) (A) |  | 5767 | 2.0 |  | 2.2 | | |  | 79.2 | 75.1 | S |
| [1H3E](http://www.rcsb.org/pdb/explore/explore.do?structureId=1H3E) (AA':B) | *T. thermophilus* tyrosyl-tRNA synthetase | tRNA-Tyr | [1H3F](http://www.rcsb.org/pdb/explore/explore.do?structureId=1H3F) (AB) |  | 3758 | 7.7 |  | 4.5 | | |  | 68.3 | 62.6 | X |
| [1H4S](http://www.rcsb.org/pdb/explore/explore.do?structureId=1H4S) (AB:T) | *T. thermophilus* prolyl-tRNA synthetase | tRNA-Pro | [1HC7](http://www.rcsb.org/pdb/explore/explore.do?structureId=1HC7) (AB) |  | 2480 | 1.0 |  | 0.9 | | |  | 88.6 | 94.5 | R |
| [1J1U](http://www.rcsb.org/pdb/explore/explore.do?structureId=1J1U) (AA':B) | *M. jannaschii* tyrosyl-tRNA synthetase | tRNA-Tyr | [1U7D](http://www.rcsb.org/pdb/explore/explore.do?structureId=1U7D) (AB) |  | 2240 | 1.3 |  | 0.8 | | |  | 73.5 | 71.6 | R |
| [1N78](http://www.rcsb.org/pdb/explore/explore.do?structureId=1N78) (A:C) | *T. thermophilus* glutamyl-tRNA synthetase | tRNA-Glu | [1J09](http://www.rcsb.org/pdb/explore/explore.do?structureId=1J09) (A) |  | 4510 | 1.9 |  | 1.4 | | |  | 86.4 | 92.4 | R |
| [1QF6](http://www.rcsb.org/pdb/explore/explore.do?structureId=1QF6) (A:B) | *E. coli* threonyl-tRNA synthetase | tRNA-Thr | [1EVL](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EVL) (A) |  | 4602 | 0.8 |  | 0.7 | | |  | 96.6 | 98.5 | R |
| [1SER](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SER) (AB:T) | *T. thermophilus* seryl-tRNA synthetase | tRNA-Ser | [1SES](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SES) (AB) |  | 2290 | 1.7 |  | 2.4 | | |  | 91.7 | 95.9 | S |
| [1U0B](http://www.rcsb.org/pdb/explore/explore.do?structureId=1U0B) (B:A) | *E. coli* cysteinyl-tRNA synthetase | tRNA-Cys | [1LI5](http://www.rcsb.org/pdb/explore/explore.do?structureId=1LI5) (B) |  | 4560 | 0.7 |  | 1.0 | | |  | 97.7 | 98.9 | R |
| [1VFG](http://www.rcsb.org/pdb/explore/explore.do?structureId=1VFG) (B:D) | *A. aeolicus* CCA-adding enzyme | tRNA | [4WBY](http://www.rcsb.org/pdb/explore/explore.do?structureId=4WBY) (A) |  | 1664 | 1.6 |  | 1.4 | | |  | 90.8 | 95.1 | R |
| [2AZX](http://www.rcsb.org/pdb/explore/explore.do?structureId=2AZX) (AA':C) | *H. sapiens* tryptophanyl-tRNA synthetase | tRNA-Trp | [1R6U](http://www.rcsb.org/pdb/explore/explore.do?structureId=1R6U) (AB) |  | 2130 | 0.8 |  | 0.6 | | |  | 91.5 | 96.5 | R |
| [2FK6](http://www.rcsb.org/pdb/explore/explore.do?structureId=2FK6) (A:R) | *B. subtilis* RNase Z | tRNA-Thr | [1Y44](http://www.rcsb.org/pdb/explore/explore.do?structureId=1Y44) (A) |  | 1530 | 0.7 |  | 0.8 | | |  | 97.6 | 98.8 | R |
| [3ADB](http://www.rcsb.org/pdb/explore/explore.do?structureId=3ADB) (A:C) | *M. jannaschii* O-phosphoseryl-tRNA kinase | tRNA-Sec | [3A4M](http://www.rcsb.org/pdb/explore/explore.do?structureId=3A4M) (A) |  | 3099 | 22.4 |  | 27.3 | | |  | 72.8 | 70.2 | X |
| [3AMT](http://www.rcsb.org/pdb/explore/explore.do?structureId=3AMT) (A:B) | *A. fulgidus* agmatinylcytidine synthetase TiaS | tRNA-Ile | [3AU7](http://www.rcsb.org/pdb/explore/explore.do?structureId=3AU7) (A) |  | 3821 | 0.8 |  | 0.7 | | |  | 95.6 | 93.6 | R |
| [4YCP](http://www.rcsb.org/pdb/explore/explore.do?structureId=4YCP) (A:B) | *E. coli* tRNA-dihydrouridine synthase C | tRNA-Trp | [4BFA](http://www.rcsb.org/pdb/explore/explore.do?structureId=4BFA) (A) |  | 2151 | 0.4 |  | 6.8 | | |  | 99.8 | 99.9 | X |
| [4YVJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=4YVJ) (AB:C) | *H. influenzae* tRNA methyltransferase D | tRNA | [3AXZ](http://www.rcsb.org/pdb/explore/explore.do?structureId=3AZX) (AA') |  | 2313 | 0.7 |  | 1.3 | | |  | 96.0 | 98.4 | R |
| [5HR7](http://www.rcsb.org/pdb/explore/explore.do?structureId=5HR7) (A:D) | *E. coli* RNA methyltransferaseRlmN | tRNA-Glu | [3RFA](http://www.rcsb.org/pdb/explore/explore.do?structureId=3RFA) (A) |  | 3450 | 1.4 |  | 1.3 | | |  | 93.7 | 96.7 | R |
| **(B) Ribosomal proteins (2)** | | | | | | | | | | | | | | |
| [1SDS](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SDS) (C:FF') | *M. jannaschii* 50S ribosomal protein L7Ae | box H/ACA sRNA | [1XBI](http://www.rcsb.org/pdb/explore/explore.do?structureId=1XBI) (A) |  | 1200 | 0.3 |  | 0.4 | | |  | 100.0 | 100.0 | R |
| [2HW8](http://www.rcsb.org/pdb/explore/explore.do?structureId=2HW8) (A:B) | *T. thermophilus* ribosomal protein L1 | mRNA | [1AD2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1AD2) (A) |  | 2401 | 6.7 |  | 5.1 | | |  | 64.6 | 47.4 | X |
| **(C) Duplex RNA (32)** | | | | | | | | | | | | | | |
| [1MSW](http://www.rcsb.org/pdb/explore/explore.do?structureId=1MSW) (D:R) | Phage T7 RNA polymerase | RNA transcript | [1ARO](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ARO) (P) |  | 1830 | 3.5 |  | 3.5 | | |  | 57.1 | 54.1 | X |
| [1N35](http://www.rcsb.org/pdb/explore/explore.do?structureId=1N35) (A:BC) | Reovirus polymerase | dsRNA | [1MUK](http://www.rcsb.org/pdb/explore/explore.do?structureId=1MUK) (A) |  | 3240 | 0.5 |  | 0.9 | | |  | 99.3 | 99.7 | R |
| [1Q2R](http://www.rcsb.org/pdb/explore/explore.do?structureId=1Q2R) (AB:E) | *Z. mobilis* guanine transglycosylase | 20-mer tRNA fragment | [1R5Y](http://www.rcsb.org/pdb/explore/explore.do?structureId=1R5Y) (AA') |  | 3006 | 0.6 |  | 1.6 | | |  | 98.0 | 99.0 | S |
| [1WNE](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WNE) (A:BC) | Foot-and-mouth disease virus polymerase | template-primer RNA decanucleotide | [1U09](http://www.rcsb.org/pdb/explore/explore.do?structureId=1U09) (A) |  | 3080 | 0.7 |  | 0.6 | | |  | 97.2 | 99.0 | R |
| [1YVP](http://www.rcsb.org/pdb/explore/explore.do?structureId=1YVP) (B:EFH) | *X. laevis* Ro autoantigen | Y RNA | [1YVR](http://www.rcsb.org/pdb/explore/explore.do?structureId=1YVR) (A) |  | 4207 | 1.4 |  | 1.3 | | |  | 90.6 | 95.2 | R |
| [1ZBI](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZBI) (A:CD) | *B. halodurans* RNase H | A form RNA | [1ZBF](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZBF) (A) |  | 1675 | 0.6 |  | 0.6 | | |  | 98.7 | 99.5 | R |
| [2AZ0](http://www.rcsb.org/pdb/explore/explore.do?structureId=2AZ0) (AB:CD) | Flock house virus B2 | siRNA | [2B9Z](http://www.rcsb.org/pdb/explore/explore.do?structureId=2B9Z) (AB) |  | 2264 | 1.3 |  | 1.0 | | |  | 85.5 | 93.3 | R |
| [2BGG](http://www.rcsb.org/pdb/explore/explore.do?structureId=2BGG) (A:PQ) | *A. fulgidus* PIWI | siRNA | [1W9H](http://www.rcsb.org/pdb/explore/explore.do?structureId=1W9H) (A) |  | 2240 | 0.9 |  | 0.8 | | |  | 96.5 | 98.2 | R |
| [2EZ6](http://www.rcsb.org/pdb/explore/explore.do?structureId=2EZ6) (AB:CD) | *A. aeolicus* RNase III | 28-mer RNA | [1JFZ](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JFZ) (AB) |  | 5193 | 1.0 |  | 0.8 | | |  | 95.5 | 84.9 | R |
| [2F8S](http://www.rcsb.org/pdb/explore/explore.do?structureId=2F8S) (AB:CD) | *A. aeolicus* argonaute | siRNA | [1YVU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1YVU) (A) |  | 990 | 1.9 |  | 1.5 | | |  | 77.4 | 78.3 | S |
| [2GJW](http://www.rcsb.org/pdb/explore/explore.do?structureId=2GJW) (AB:EFH) | *A. fulgidus* splicing endonuclease | bulge-helix-bulge RNA | [1R0V](http://www.rcsb.org/pdb/explore/explore.do?structureId=1R0V) (AB) |  | 3243 | 1.0 |  | 1.0 | | |  | 83.0 | 91.7 | R |
| [2GXB](http://www.rcsb.org/pdb/explore/explore.do?structureId=2GXB) (A:EF) | *H. sapiens* Z alpha domain of adenosine deaminase | dsRNA | [**1QGP**](http://www.rcsb.org/pdb/explore/explore.do?structureId=1QGP) **(A)** |  | 768 | 1.1 |  | 0.7 | | |  | 87.9 | 90.9 | R |
| [2QUX](http://www.rcsb.org/pdb/explore/explore.do?structureId=2QUX) (AB:C) | Pseudomonas phage PP7 coat protein | hairpin RNA | [2QUD](http://www.rcsb.org/pdb/explore/explore.do?structureId=2QUD) (AB) |  | 1754 | 0.9 |  | 0.5 | | |  | 96.9 | 98.4 | R |
| [2Y8W](http://www.rcsb.org/pdb/explore/explore.do?structureId=2Y8W) (A:B) | *T. thermophilus* endoribonuclease Cse3 | hairpin RNA | [1WJ9](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WJ9) (A) |  | 3258 | 1.1 |  | 3.1 | | |  | 95.5 | 97.3 | X |
| [2ZKO](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZKO) (AB:CD) | NS1 protein of influenza A | A-form dsRNA | [2Z0A](http://www.rcsb.org/pdb/explore/explore.do?structureId=2Z0A) (AB) |  | 2466 | 0.6 |  | 0.8 | | |  | 97.7 | 98.8 | R |
| [3BSN](http://www.rcsb.org/pdb/explore/explore.do?structureId=3BSN) (A:PT) | Norwalk virus polymerase | synthetic RNA | [1SH3](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SH3) (A) |  | 3111 | 1.3 |  | 1.9 | | |  | 90.9 | 95.2 | S |
| [3DD2](http://www.rcsb.org/pdb/explore/explore.do?structureId=3DD2) (H:B) | *H. sapiens* thrombin | 26-mer RNA | [1JOU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JOU) (D) |  | 1822 | 0.6 |  | 0.5 | | |  | 96.5 | 98.1 | R |
| [3EQT](http://www.rcsb.org/pdb/explore/explore.do?structureId=3EQT) (AB:CD) | *H. sapiens* helicase DHX58 | dsRNA | [2W4R](http://www.rcsb.org/pdb/explore/explore.do?structureId=2W4R) (AA') |  | 2705 | 1.2 |  | 1.2 | | |  | 47.9 | 42.5 | R |
| [3FTE](http://www.rcsb.org/pdb/explore/explore.do?structureId=3FTE) (A:CD) | *A. aeolicus* methyltransferase KsgA | rRNA | [3FTD](http://www.rcsb.org/pdb/explore/explore.do?structureId=3FTD) (A) |  | 836 | 1.4 |  | 1.1 | | |  | 89.7 | 94.9 | R |
| [3KS8](http://www.rcsb.org/pdb/explore/explore.do?structureId=3KS8) (AB:EF) | *R. ebolavirus* polymerase cofactor VP35 | dsRNA | [3KS4](http://www.rcsb.org/pdb/explore/explore.do?structureId=3KS4) (AB) |  | 1663 | 0.6 |  | 0.4 | | |  | 49.8 | 50.1 | R |
| [3MOJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=3MOJ) (B:A) | *B. subtilis* helicase dbpA | *E.coli* 23S rRNA fragment | [2G0C](http://www.rcsb.org/pdb/explore/explore.do?structureId=2G0C) (A) |  | 1758 | 1.0 |  | 1.0 | | |  | 94.5 | 97.6 | R |
| [3O3I](http://www.rcsb.org/pdb/explore/explore.do?structureId=3O3I) (X:A) | *H. sapiens* Hiwi1 PAZ domain | piRNA | [**2L5C**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2L5C) **(A)** |  | 923 | 2.1 |  | 2.7 | | |  | 79.0 | 84.5 | S |
| [3OIJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=3OIJ) (AB:C) | *S. cerevisiae* methyltransferase | SSU rRNA | [3OII](http://www.rcsb.org/pdb/explore/explore.do?structureId=3OII) (AB) |  | 2070 | 0.8 |  | 1.7 | | |  | 97.0 | 98.5 | S |
| [3OL6](http://www.rcsb.org/pdb/explore/explore.do?structureId=3OL6) (A:BCD) | Poliovirus polymerase | synthetic RNA | [1RA6](http://www.rcsb.org/pdb/explore/explore.do?structureId=1RA6) (A) |  | 4174 | 0.8 |  | 1.1 | | |  | 94.9 | 97.8 | R |
| [3RW6](http://www.rcsb.org/pdb/explore/explore.do?structureId=3RW6) (A:H) | *H. sapiens* nuclear RNA export factor 1 | CTE RNA | [3RW7](http://www.rcsb.org/pdb/explore/explore.do?structureId=3RW7) (A) |  | 2699 | 13.5 |  | 19.0 | | |  | 66.4 | 64.4 | X |
| [4ERD](http://www.rcsb.org/pdb/explore/explore.do?structureId=4ERD) (AB:CD) | *T. thermophila* p65 C-terminal domain | stem IV of telomerase RNA | [4EYT](http://www.rcsb.org/pdb/explore/explore.do?structureId=4EYT) (AB) |  | 3280 | 1.5 |  | 1.2 | | |  | 47.0 | 46.5 | R |
| [4FVU](http://www.rcsb.org/pdb/explore/explore.do?structureId=4FVU) (A:BC) | Lassa virus *e*xonuclease | dsRNA | [3Q7C](http://www.rcsb.org/pdb/explore/explore.do?structureId=3Q7C) (A) |  | 1240 | 1.0 |  | 0.7 | | |  | 97.2 | 98.5 | R |
| [4IG8](http://www.rcsb.org/pdb/explore/explore.do?structureId=4IG8) (A:BC) | *H. sapiens* oligoadenylate synthetase 1 | dsRNA | [1PX5](http://www.rcsb.org/pdb/explore/explore.do?structureId=1PX5) (A) |  | 2914 | 2.4 |  | 2.8 | | |  | 79.0 | 74.4 | S |
| [4ILL](http://www.rcsb.org/pdb/explore/explore.do?structureId=4ILL) (AB:RC) | *S. solfataricus* endoribonuclease Cas6 | CRISPR RNA | [4ILR](http://www.rcsb.org/pdb/explore/explore.do?structureId=4ILR) (AA') |  | 7074 | 0.9 |  | 0.9 | | |  | 96.3 | 98.1 | R |
| [4ZT0](http://www.rcsb.org/pdb/explore/explore.do?structureId=4ZT0) (A:B) | *S. pyogenes* CRISPR-associated endonuclease Cas9 | single-guide RNA | [4CMP](http://www.rcsb.org/pdb/explore/explore.do?structureId=4CMP) (A) |  | 10845 | 29.6 |  | 22.0 | | |  | 45.6 | 43.1 | X |
| [5ED1](http://www.rcsb.org/pdb/explore/explore.do?structureId=5ED1) (A:BC) | *H. sapiens* ADAR2 | *S. cerevisiae* dsRNA | [1ZY7](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZY7) (A) |  | 2403 | 1.1 |  | 2.3 | | |  | 95.4 | 97.5 | S |
| [5F5H](http://www.rcsb.org/pdb/explore/explore.do?structureId=5F5H) (A:C) | *M. musculus* Roquin-1 | Ox40 3'-UTR | [4QI0](http://www.rcsb.org/pdb/explore/explore.do?structureId=4QIO) (A) |  | 1618 | 0.5 |  | 0.6 | | |  | 99.2 | 99.6 | R |
| **(D) Single-stranded RNA (45)** | | | | | | | | | | | | | | |
| [1AV6](http://www.rcsb.org/pdb/explore/explore.do?structureId=1AV6) (A:B) | Vaccinia virus cap-specific mRNA methyltransferase | M7G capped RNA | [1B42](http://www.rcsb.org/pdb/explore/explore.do?structureId=1B42) (A) |  | 844 | 0.5 |  | 0.4 | | |  | 99.1 | 99.6 | R |
| [1C9S](http://www.rcsb.org/pdb/explore/explore.do?structureId=1C9S) (L:W1-7) | *G. stearothermophilus*TRAP | ssRNA | [2EXT](http://www.rcsb.org/pdb/explore/explore.do?structureId=2EXT) (A) |  | 1027 | 0.3 |  | 0.2 | | |  | 100.0 | 100.0 | R |
| [1CVJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=1CVJ) (A:M) | *H. sapiens* poly(A)-binding protein | polyA | [4F25](http://www.rcsb.org/pdb/explore/explore.do?structureId=4F25) (A) |  | 2822 | 2.7 |  | 3.9 | | |  | 93.4 | 93.9 | X |
| [1G2E](http://www.rcsb.org/pdb/explore/explore.do?structureId=1G2E) (A:B) | *H. sapiens* RRM domain of the HuD protein | class II ARE fragment | [4EGL](http://www.rcsb.org/pdb/explore/explore.do?structureId=4EGL) (A) |  | 2776 | 0.9 |  | 0.6 | | |  | 49.8 | 49.8 | R |
| [1K8W](http://www.rcsb.org/pdb/explore/explore.do?structureId=1K8W) (A:B) | *E. coli p*seudouridine synthase B | T stem-loop RNA | [1R3F](http://www.rcsb.org/pdb/explore/explore.do?structureId=1R3F) (A) |  | 2973 | 1.9 |  | 1.3 | | |  | 80.8 | 90.3 | R |
| [1KQ2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1KQ2) (ABHIKM:R) | *S. aureus* Hfq | 7-mer RNA | [1KQ1](http://www.rcsb.org/pdb/explore/explore.do?structureId=1KQ1) (ABHIKM) |  | 3026 | 0.6 |  | 0.5 | | |  | 81.9 | 91.8 | R |
| [1M5O](http://www.rcsb.org/pdb/explore/explore.do?structureId=1M5O) (C:B) | *H. sapiens* U1 Snp A | hairpin ribozyme | [1OIA](http://www.rcsb.org/pdb/explore/explore.do?structureId=1OIA) (A) |  | 1770 | 1.2 |  | 0.9 | | |  | 96.6 | 98.1 | R |
| [1M8V](http://www.rcsb.org/pdb/explore/explore.do?structureId=1M8V) (AM:O) | *P. abyssi* Sm | uridine heptamer | [1H64](http://www.rcsb.org/pdb/explore/explore.do?structureId=1H64) (AM) |  | 1290 | 0.6 |  | 0.4 | | |  | 62.2 | 61.2 | R |
| [1M8W](http://www.rcsb.org/pdb/explore/explore.do?structureId=1M8W) (A:CE) | *H. sapiens* pumilio-homology domain | Nre1-19 RNA | [1M8Z](http://www.rcsb.org/pdb/explore/explore.do?structureId=1M8Z) (A) |  | 2110 | 0.8 |  | 0.7 | | |  | 90.9 | 96.0 | R |
| [1UVI](http://www.rcsb.org/pdb/explore/explore.do?structureId=1UVI) (A:D) | phi6 RNA polymerase | 6-mer RNA | [1HHS](http://www.rcsb.org/pdb/explore/explore.do?structureId=1HHS) (A) |  | 1814 | 0.2 |  | 0.2 | | |  | 100.0 | 100.0 | R |
| [1WPU](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WPU) (A:C) | *B. subtilis* HutP antitermination protein | hut mRNA | [1WPV](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WPV) (A) |  | 1360 | 0.2 |  | 0.2 | | |  | 100.0 | 100.0 | R |
| [2A8V](http://www.rcsb.org/pdb/explore/explore.do?structureId=2A8V) (B:E) | *E. coli* RHO | Cytosine rich RNA | [1A8V](http://www.rcsb.org/pdb/explore/explore.do?structureId=1A8V) (B) |  | 720 | 1.0 |  | 1.6 | | |  | 94.7 | 97.7 | S |
| [2ASB](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ASB) (A:B) | *M. tuberculosis* Nus A antiterminator | BoxC rRNA | [1K0R](http://www.rcsb.org/pdb/explore/explore.do?structureId=1K0R) (A) |  | 2320 | 1.1 |  | 0.8 | | |  | 91.8 | 96.4 | R |
| [2GIC](http://www.rcsb.org/pdb/explore/explore.do?structureId=2GIC) (A:R) | VSV nucleocapsid | viral genomic RNA | [2QVJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=2QVJ) (A) |  | 2000 | 1.3 |  | 0.9 | | |  | 91.9 | 95.7 | R |
| [2IX1](http://www.rcsb.org/pdb/explore/explore.do?structureId=2IX1) (A:B) | *E. coli* RNase II | polyA | [2IX0](http://www.rcsb.org/pdb/explore/explore.do?structureId=2IX0) (A) |  | 4160 | 1.6 |  | 0.9 | | |  | 86.2 | 93.3 | R |
| [2JEA](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JEA) (AB:C) | *S. solfataricus* exosome | substrate RNA | [2JE6](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JE6) (AB) |  | 1533 | 0.3 |  | 0.3 | | |  | 99.8 | 99.9 | R |
| [2JLU](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JLU) (A:C) | Dengue virus serine protease subunit NS3 | ssRNA | [2JLQ](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JLQ) (A) |  | 1925 | 2.1 |  | 2.8 | | |  | 74.3 | 78.1 | S |
| [2PY9](http://www.rcsb.org/pdb/explore/explore.do?structureId=2PY9) (B:E) | *H. sapiens* poly(rC)-binding protein 2 | human telomeric RNA | [**2JZX**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JZX) **(A:1-73)** |  | 1060 | 1.4 |  | 1.6 | | |  | 85.5 | 92.0 | R |
| [2Q66](http://www.rcsb.org/pdb/explore/explore.do?structureId=2Q66) (A:X) | *S. cerevisiae* poly(A) polymerase | polyA | [2HHP](http://www.rcsb.org/pdb/explore/explore.do?structureId=2HHP) (A) |  | 1811 | 1.9 |  | 2.1 | | |  | 85.0 | 91.5 | S |
| [2R7R](http://www.rcsb.org/pdb/explore/explore.do?structureId=2R7R) (A:X) | Rotavirus polymerase VP1 | RNA | [2R7Q](http://www.rcsb.org/pdb/explore/explore.do?structureId=2R7Q) (A) |  | 1955 | 0.2 |  | 1.9 | | |  | 98.7 | 99.3 | S |
| [2XGJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=2XGJ) (A:C) | *S. cerevisiae* Mtr4 | polyA | [4U4C](http://www.rcsb.org/pdb/explore/explore.do?structureId=4U4C) (A) |  | 1389 | 4.1 |  | 3.1 | | |  | 71.5 | 65.5 | X |
| [2XNR](http://www.rcsb.org/pdb/explore/explore.do?structureId=2XNR) (A:C) | *S. cerevisiae* Nab3-RRM | UCUU recognition sequence | [2XNQ](http://www.rcsb.org/pdb/explore/explore.do?structureId=2XNQ) (A) |  | 926 | 1.0 |  | 1.2 | | |  | 94.3 | 97.4 | R |
| [2XZO](http://www.rcsb.org/pdb/explore/explore.do?structureId=2XZO) (A:D) | *H. sapiens* Upf1 helicase | polyU | [2XZP](http://www.rcsb.org/pdb/explore/explore.do?structureId=2XZP) (A) |  | 2006 | 6.2 |  | 5.0 | | |  | 57.2 | 54.2 | X |
| [3AEV](http://www.rcsb.org/pdb/explore/explore.do?structureId=3AEV) (B:C) | *P. horikoshii* Dim2p | *P. horikoshii* 16S rRNA fragment | [2E3U](http://www.rcsb.org/pdb/explore/explore.do?structureId=2E3U) (A) |  | 2416 | 0.7 |  | 0.5 | | |  | 97.4 | 99.0 | R |
| [3BX2](http://www.rcsb.org/pdb/explore/explore.do?structureId=3BX2) (A:C) | *S. cerevisiae* PUF4 | 3' UTR binding sequence | [3BWT](http://www.rcsb.org/pdb/explore/explore.do?structureId=3BWT) (A) |  | 2467 | 0.6 |  | 0.5 | | |  | 98.5 | 99.3 | R |
| [3D2S](http://www.rcsb.org/pdb/explore/explore.do?structureId=3D2S) (A:E) | *H. sapiens* MBNL1 ZnF3/4 | pre-mRNA | [3D2Q](http://www.rcsb.org/pdb/explore/explore.do?structureId=3D2Q) (A) |  | 569 | 0.8 |  | 0.6 | | |  | 97.0 | 98.7 | R |
| [3MDG](http://www.rcsb.org/pdb/explore/explore.do?structureId=3MDG) (AB:C) | *H. sapiens* CFI(m)25 | pre-mRNA | [3BAP](http://www.rcsb.org/pdb/explore/explore.do?structureId=3BAP) (AA') |  | 1069 | 0.5 |  | 0.9 | | |  | 96.5 | 98.1 | R |
| [3NMR](http://www.rcsb.org/pdb/explore/explore.do?structureId=3NMR) (A:B) | *H. sapiens* CUG-binding protein 1 | UGU-rich mRNA | [**2DHS**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2DHS) **(A)** |  | 1096 | 2.7 |  | 2.2 | | |  | 43.0 | 39.7 | S |
| [3O8C](http://www.rcsb.org/pdb/explore/explore.do?structureId=3O8C) (A:C) | HCV NS3 helicase | polyU | [3O8B](http://www.rcsb.org/pdb/explore/explore.do?structureId=3O8B) (A) |  | 1909 | 1.0 |  | 1.1 | | |  | 94.6 | 97.5 | R |
| [3PF4](http://www.rcsb.org/pdb/explore/explore.do?structureId=3PF4) (B:R) | *B. subtilis* CspB | ssRNA | [1CSP](http://www.rcsb.org/pdb/explore/explore.do?structureId=1CSP) (A) |  | 963 | 0.5 |  | 0.4 | | |  | 98.5 | 99.4 | R |
| [3QJJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=3QJJ) (A:Q) | *P. horikoshii* RAMP Protein | CRISPR repeat RNA | [3UFC](http://www.rcsb.org/pdb/explore/explore.do?structureId=3UFC) (X) |  | 3191 | 1.0 |  | 1.0 | | |  | 96.0 | 98.3 | R |
| [3RC8](http://www.rcsb.org/pdb/explore/explore.do?structureId=3RC8) (A:E) | *H. sapiens* helicase SUPV3L1 | RNA fragment | [3RC3](http://www.rcsb.org/pdb/explore/explore.do?structureId=3RC3) (A) |  | 1471 | 1.1 |  | 0.8 | | |  | 92.3 | 96.3 | R |
| [4E78](http://www.rcsb.org/pdb/explore/explore.do?structureId=4E78) (A:PT) | HCV polymerase | RNA primer-template pair | [4E76](http://www.rcsb.org/pdb/explore/explore.do?structureId=4E76) (A) |  | 2100 | 0.7 |  | 0.8 | | |  | 98.4 | 99.4 | R |
| [4H5P](http://www.rcsb.org/pdb/explore/explore.do?structureId=4HSP) (AB:E) | Rift valley fever virus nucleocapsid | polyU | [3LYF](http://www.rcsb.org/pdb/explore/explore.do?structureId=3LYF) (AB) |  | 4482 | 0.9 |  | 2.1 | | |  | 42.5 | 42.6 | S |
| [4HOR](http://www.rcsb.org/pdb/explore/explore.do?structureId=4HOR) (A:X) | *H. sapiens* IFIT | polyC | [4HOQ](http://www.rcsb.org/pdb/explore/explore.do?structureId=4HOQ) (A) |  | 1747 | 3.1 |  | 2.4 | | |  | 68.7 | 72.5 | S |
| [4J7M](http://www.rcsb.org/pdb/explore/explore.do?structureId=4J7M) (A:B) | *M. musculus* Dom3Z | polyU | [4J7N](http://www.rcsb.org/pdb/explore/explore.do?structureId=4J7N) (A) |  | 1268 | 0.3 |  | 0.3 | | |  | 99.7 | 99.9 | R |
| [4M59](http://www.rcsb.org/pdb/explore/explore.do?structureId=4M59) (AB:CD) | *Z. mays* chloroplast ppr10 | psaJ RNA | [4M57](http://www.rcsb.org/pdb/explore/explore.do?structureId=4M57) (AA') |  | 7842 | 10.5 |  | 7.1 | | |  | 30.1 | 26.1 | X |
| [4MDX](http://www.rcsb.org/pdb/explore/explore.do?structureId=4MDX) (AB:C) | *B. subtilis* mRNA interferase MazF | mRNA | [1NE8](http://www.rcsb.org/pdb/explore/explore.do?structureId=1NE8) (AA') |  | 2127 | 0.7 |  | 1.6 | | |  | 98.4 | 86.4 | S |
| [4N2Q](http://www.rcsb.org/pdb/explore/explore.do?structureId=4N2Q) (A:B) | *B. distachyon* thylakoid assembly 8 | Zm4 13-mer RNA | [4ME2](http://www.rcsb.org/pdb/explore/explore.do?structureId=4ME2) (A) |  | 814 | 2.3 |  | 1.3 | | |  | 78.6 | 82.3 | R |
| [4QU6](http://www.rcsb.org/pdb/explore/explore.do?structureId=4QU6) (A:B) | *H. sapiens* GRSF1 | synthetic RNA | [**2LMI**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2LMI) **(A)** |  | 696 | 2.5 |  | 2.4 | | |  | 80.8 | 80.6 | S |
| [5BUD](http://www.rcsb.org/pdb/explore/explore.do?structureId=5BUD) (A:B) | *C. albicans* decapping nuclease RAI1 | polyU | [5BTH](http://www.rcsb.org/pdb/explore/explore.do?structureId=5BTH) (A) |  | 1262 | 0.5 |  | 1.2 | | |  | 99.5 | 99.8 | R |
| [5DET](http://www.rcsb.org/pdb/explore/explore.do?structureId=5DET) (AB:PQ) | *H. sapiens* RBPMS | CAC containing ssRNA | [5CYJ](http://www.rcsb.org/pdb/explore/explore.do?structureId=5CYJ) (AB) |  | 2137 | 1.2 |  | 1.6 | | |  | 46.9 | 47.6 | S |
| [5EIM](http://www.rcsb.org/pdb/explore/explore.do?structureId=5EIM) (A:C) | *S. pombe* YTH domain of spMmi1 | synthetic RNA | [5H8A](http://www.rcsb.org/pdb/explore/explore.do?structureId=5H8A) (A) |  | 1529 | 0.6 |  | 1.3 | | |  | 98.2 | 99.3 | R |
| [5ELS](http://www.rcsb.org/pdb/explore/explore.do?structureId=5ELS) (AC:HI) | *H. sapiens* KH domain of T-STAR | synthetic RNA | [5EL3](http://www.rcsb.org/pdb/explore/explore.do?structureId=5EL3) (AB) |  | 2313 | 1.5 |  | 2.9 | | |  | 47.7 | 49.1 | S |
| [5EX7](http://www.rcsb.org/pdb/explore/explore.do?structureId=5EX7) (A:B) | *D. melanogaster* Brat NHL domain | hunchback mRNA | [4ZLR](http://www.rcsb.org/pdb/explore/explore.do?structureId=4ZLR) (A) |  | 1639 | 0.4 |  | 0.6 | | |  | 99.8 | 99.9 | R |
| **III. Bound-Unbound cases (10)** | | | | | | | | | | | | | | |
| **(A) Complexes with tRNA (2)** | | | | | | | | | | | | | | |
| [2ZM5](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZM5) (A:C) | *E. coli* iso-pent-enyl-transferase | tRNA-Phe |  | [3L0U](http://www.rcsb.org/pdb/explore/explore.do?structureId=3L0U) (A) | 3936 |  | 4.2 | 6.5 | | |  |  |  |  |
| [3ZJT](http://www.rcsb.org/pdb/explore/explore.do?structureId=3ZJT) (A:B) | *E. coli* leucyl-tRNA synthetase | tRNA-Leu |  | [2NQP](http://www.rcsb.org/pdb/explore/explore.do?structureId=2NQP) (F) | 4322 |  | 2.8 | 2.9 | | |  |  |  |  |
| **(C) Duplex RNA (5)** | | | | | | | | | | | | | | |
| [1HQ1](http://www.rcsb.org/pdb/explore/explore.do?structureId=1HQ1) (A:B) | *E. coli* SRP | 4.5S RNA domain IV |  | [1DUH](http://www.rcsb.org/pdb/explore/explore.do?structureId=1DUH) (A) | 1364 |  | 38.3 | 30.4 | | |  |  |  |  |
| [1JID](http://www.rcsb.org/pdb/explore/explore.do?structureId=1J1D) (A:B) | *H. sapiens* SRP19 | SRP RNA |  | [1D4R](http://www.rcsb.org/pdb/explore/explore.do?structureId=1D4R) (A) | 1436 |  | 2.6 | 4.0 | | |  |  |  |  |
| [2OZB](http://www.rcsb.org/pdb/explore/explore.do?structureId=2OZB) (AB:C) | *H. sapiens* ribonucleoprotein | U4snRNA |  | [**2XEB**](http://www.rcsb.org/pdb/explore/explore.do?structureId=2XEB) **(AB)** | 2569 |  | 11.0 | 12.5 | | |  |  |  |  |
| [2PJP](http://www.rcsb.org/pdb/explore/explore.do?structureId=2PJP) (A:B) | *E. coli* SelB | SECIS RNA |  | [**1MFK**](http://www.rcsb.org/pdb/explore/explore.do?structureId=1MFK) **(A)** | 1300 |  | 2.5 | 3.6 | | |  |  |  |  |
| [3BT7](http://www.rcsb.org/pdb/explore/explore.do?structureId=3BT7) (A:C) | *E. coli* methyltransferase TrmA | T-arm analogue |  | [1EVV](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EVV) (A) | 2230 |  | 3.1 | 3.5 | | |  |  |  |  |
| **(D) Single-stranded RNA (3)** | | | | | | | | | | | | | | |
| [1LNG](http://www.rcsb.org/pdb/explore/explore.do?structureId=1LNG) (A:B) | *M. jannaschii* SRP19 | 7S SRP RNA |  | [1Z43](http://www.rcsb.org/pdb/explore/explore.do?structureId=1Z43) (A) | 2367 |  | 2.0 | 2.1 | | |  |  |  |  |
| [2I82](http://www.rcsb.org/pdb/explore/explore.do?structureId=2I82) (A:E) | *E. coli* pseudouridine synthase RluA | tRNA-Phe |  | [3L0U](http://www.rcsb.org/pdb/explore/explore.do?structureId=3L0U) (A:26-43) | 3018 |  | 4.2 | 4.7 | | |  |  |  |  |
| [3IEV](http://www.rcsb.org/pdb/explore/explore.do?structureId=3IEV) (A:D) | *A. aeolicus* GTPase era | 16S rRNA |  | [1SDR](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SDR) (B) | 2273 |  | 7.6 | 8.4 | | |  |  |  |  |

aFour letter PDB
code of the protein-RNA complexes used in the benchmark with the chain id of
the protein and the RNA molecules in the parenthesis. For structures solved by
NMR (**shown in bold**) the closet model
to the average structure of the ensemble was considered as the reference
structure for structural alignment. Symmetry related chains are primed (For
example, A' and B' in 3HL2). If the
Unbound RNA structure is taken from another complex they are marked with \* (For
example, in 3I9C nucleotides from 1080 to 1129 are considered).

bSurface area buried
between protein and RNA upon complexation.

Crmsd calculated
considering the equivalent Cα atoms.

drmsd calculated
considering the equivalent P atoms.

ermsd
calculated considering the equivalent interface atoms.