Research workbench
Rnase R bound to a 30S degradation intermediate (State I - head-turning)
Analyse Rnase R bound to a 30S degradation intermediate (State I - head-turning) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CEE
- Type
- protein + RNA
- Length
- 4,268 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Bacillus subtilis subsp. subtilis str. 168
- Molecule
- 16S rRNA; RNA Substrate; RNase R; 30S ribosomal protein S2; 30S ribosomal protein S4; 30S…
- UniProt
- P21464, P21466, P21467, P12879, P21472, P21473, P21474, P12874, P21477, P21468, P21475, P04969, P21465, P21469, P21470, P21471, P20282, P12878, P21476
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.7 · 22 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1333 | — | — |
| B | RNA Substrate | rna | 7 | — | — |
| C | RNase R | protein | 708 | 34% helix, 28% strand | — |
| D | 30S ribosomal protein S2 | protein | 218 | 52% helix, 16% strand | P21464 |
| F | 30S ribosomal protein S4 | protein | 185 | 42% helix, 8% strand | P21466 |
| G | 30S ribosomal protein S5 | protein | 158 | 29% helix, 37% strand | P21467 |
| I | 30S ribosomal protein S8 | protein | 131 | 27% helix, 34% strand | P12879 |
| L | 30S ribosomal protein S12 | protein | 136 | 10% helix, 34% strand | P21472 |
| O | 30S ribosomal protein S15 | protein | 85 | 79% helix, 0% strand | P21473 |
| P | 30S ribosomal protein S16 | protein | 88 | 33% helix, 38% strand | P21474 |
| Q | 30S ribosomal protein S17 | protein | 84 | 0% helix, 49% strand | P12874 |
| S | 30S ribosomal protein S20 | protein | 83 | 88% helix, 0% strand | P21477 |
| T | 30S ribosomal protein S6 | protein | 95 | 32% helix, 46% strand | P21468 |
| U | 30S ribosomal protein S18 | protein | 64 | 45% helix, 3% strand | P21475 |
| V | 30S ribosomal protein S11 | protein | 101 | 31% helix, 34% strand | P04969 |
| E | 30S ribosomal protein S3 | protein | 205 | 34% helix, 26% strand | P21465 |
| H | 30S ribosomal protein S7 | protein | 149 | 58% helix, 9% strand | P21469 |
| J | 30S ribosomal protein S9 | protein | 108 | 42% helix, 26% strand | P21470 |
| K | 30S ribosomal protein S10 | protein | 95 | 28% helix, 53% strand | P21471 |
| M | 30S ribosomal protein S13 | protein | 108 | 47% helix, 2% strand | P20282 |
| N | 30S ribosomal protein S14 | protein | 49 | 20% helix, 6% strand | P12878 |
| R | 30S ribosomal protein S19 | protein | 78 | 24% helix, 19% strand | P21476 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.87 | 0.89 | 101 | empty |
| 2 | 666 | 0.85 | 0.90 | 70 | empty |
| 3 | 619 | 0.83 | 0.89 | 41 | empty |
| 4 | 872 | 0.83 | 0.86 | 79 | empty |
| 5 | 995 | 0.83 | 0.84 | 86 | empty |
Interfaces
38 interfaces between chains.
- A–L · 3025 Ų buried · 87 hydrogen bonds · protein-nucleic
- A–F · 2626 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–P · 2381 Ų buried · 62 hydrogen bonds · protein-nucleic
- A–Q · 2100 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–S · 1985 Ų buried · 58 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- P21464 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S2 (P21464) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P21468 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S6 (P21468) · a predicted model of the same protein · chain T against A, TM-score 0.99
- P21470 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S9 (P21470) · a predicted model of the same protein · chain J against A, TM-score 0.99
- P12879 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P12879) · a predicted model of the same protein · chain I against A, TM-score 0.99
- P04969 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S11 (P04969) · a predicted model of the same protein · chain V against A, TM-score 0.99
- P21472 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S12 (P21472) · a predicted model of the same protein · chain L against A, TM-score 0.98
- P21466 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S4 (P21466) · a predicted model of the same protein · chain F against A, TM-score 0.98
- P21474 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (P21474) · a predicted model of the same protein · chain P against A, TM-score 0.98
- P21467 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (P21467) · a predicted model of the same protein · chain G against A, TM-score 0.98
- P21473 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (P21473) · a predicted model of the same protein · chain O against A, TM-score 0.98
- P21475 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S18 (P21475) · a predicted model of the same protein · chain U against A, TM-score 0.98
- P21465 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (P21465) · a predicted model of the same protein · chain E against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21464
- Every structure of UniProt P21466
- Every structure of UniProt P21467
- Every structure of UniProt P12879
- Every structure of UniProt P21472
- Every structure of UniProt P21473
- Every structure of UniProt P21474
- Every structure of UniProt P12874
- Every structure of UniProt P21477
- Every structure of UniProt P21468
- Every structure of UniProt P21475
- Every structure of UniProt P04969
- Every structure of UniProt P21465
- Every structure of UniProt P21469
- Every structure of UniProt P21470
- Every structure of UniProt P21471
- Every structure of UniProt P20282
- Every structure of UniProt P12878
- Every structure of UniProt P21476
- Elsewhere: RCSB PDB 8CEE · PDBe 8CEE · UniProt P21464 · UniProt P21466 · UniProt P21467 · UniProt P12879 · UniProt P21472 · UniProt P21473 · UniProt P21474 · UniProt P12874 · UniProt P21477 · UniProt P21468 · UniProt P21475 · UniProt P04969 · UniProt P21465 · UniProt P21469 · UniProt P21470 · UniProt P21471 · UniProt P20282 · UniProt P12878 · UniProt P21476
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