Research workbench
Cryo-EM structure of a Staphylococus aureus 30S-RbfA complex
Analyse Cryo-EM structure of a Staphylococus aureus 30S-RbfA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BYV
- Type
- protein + RNA
- Length
- 3,924 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Staphylococcus aureus subsp. aureus NCTC 8325
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- Q2FZ25, Q2FW12, Q2FXK6, Q2FW23, Q2G113, P48940, Q2FW20, Q2FW39, Q931G5, Q2FW31, P0A0H0, Q2FW30, Q2FW19, Q2G2Q1, Q2FZ45, Q2FW15, Q2G111, Q2FW10, Q2FXY6, Q2G2Q4
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 2.89 · 21 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | 16S ribosomal RNA | rna | 1533 | — | — |
| b | 30S ribosomal protein S2 | protein | 222 | 47% helix, 11% strand | Q2FZ25 |
| c | 30S ribosomal protein S3 | protein | 204 | 34% helix, 23% strand | Q2FW12 |
| d | 30S ribosomal protein S4 | protein | 197 | 40% helix, 9% strand | Q2FXK6 |
| e | 30S ribosomal protein S5 | protein | 154 | 28% helix, 34% strand | Q2FW23 |
| f | 30S ribosomal protein S6 | protein | 94 | 28% helix, 36% strand | Q2G113 |
| g | 30S ribosomal protein S7 | protein | 140 | 62% helix, 3% strand | P48940 |
| h | 30S ribosomal protein S8 | protein | 131 | 28% helix, 33% strand | Q2FW20 |
| i | 30S ribosomal protein S9 | protein | 128 | 34% helix, 16% strand | Q2FW39 |
| j | 30S ribosomal protein S10 | protein | 99 | 24% helix, 28% strand | Q931G5 |
| k | 30S ribosomal protein S11 | protein | 118 | 24% helix, 23% strand | Q2FW31 |
| l | 30S ribosomal protein S12 | protein | 135 | 6% helix, 29% strand | P0A0H0 |
| m | 30S ribosomal protein S13 | protein | 110 | 32% helix, 0% strand | Q2FW30 |
| n | 30S ribosomal protein S14 type Z | protein | 60 | 28% helix, 7% strand | Q2FW19 |
| o | 30S ribosomal protein S15 | protein | 88 | 74% helix, 0% strand | Q2G2Q1 |
| p | 30S ribosomal protein S16 | protein | 90 | 30% helix, 22% strand | Q2FZ45 |
| q | 30S ribosomal protein S17 | protein | 85 | 0% helix, 59% strand | Q2FW15 |
| r | 30S ribosomal protein S18 | protein | 58 | 45% helix, 3% strand | Q2G111 |
| s | 30S ribosomal protein S19 | protein | 82 | 21% helix, 11% strand | Q2FW10 |
| t | 30S ribosomal protein S20 | protein | 80 | 74% helix, 0% strand | Q2FXY6 |
| A | Ribosome-binding factor A | protein | 116 | 51% helix, 16% strand | Q2G2Q4 |
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 | 1091 | 0.85 | 0.87 | 97 | empty |
| 2 | 885 | 0.83 | 0.86 | 66 | empty |
| 3 | 1105 | 0.83 | 0.85 | 67 | empty |
| 4 | 754 | 0.82 | 0.86 | 72 | empty |
| 5 | 391 | 0.82 | 0.92 | 56 | empty |
Interfaces
42 interfaces between chains.
- a–l · 3258 Ų buried · 82 hydrogen bonds · protein-nucleic
- a–d · 3046 Ų buried · 79 hydrogen bonds · protein-nucleic
- a–i · 2948 Ų buried · 73 hydrogen bonds · protein-nucleic
- a–p · 2501 Ų buried · 59 hydrogen bonds · protein-nucleic
- a–t · 2265 Ų buried · 40 hydrogen bonds · protein-nucleic
Compared structures
- Q2FW20 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (Q2FW20) · a predicted model of the same protein · chain h against A, TM-score 0.98
- P0A0H0 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S12 (P0A0H0) · a predicted model of the same protein · chain l against A, TM-score 0.98
- Q2G2Q1 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (Q2G2Q1) · a predicted model of the same protein · chain o against A, TM-score 0.97
- Q2FXK6 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S4 (Q2FXK6) · a predicted model of the same protein · chain d against A, TM-score 0.97
- Q2FW23 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (Q2FW23) · a predicted model of the same protein · chain e against A, TM-score 0.96
- Q2FW12 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (Q2FW12) · a predicted model of the same protein · chain c against A, TM-score 0.95
- Q2FZ45 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (Q2FZ45) · a predicted model of the same protein · chain p against A, TM-score 0.95
- Q2G111 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S18 (Q2G111) · a predicted model of the same protein · chain r against A, TM-score 0.94
- Q2FW15 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S17 (Q2FW15) · a predicted model of the same protein · chain q against A, TM-score 0.94
- Q2FW31 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S11 (Q2FW31) · a predicted model of the same protein · chain k against A, TM-score 0.94
- Q2G113 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S6 (Q2G113) · a predicted model of the same protein · chain f against A, TM-score 0.93
- Q2FXY6 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S20 (Q2FXY6) · a predicted model of the same protein · chain t against A, TM-score 0.93
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 Q2FZ25
- Every structure of UniProt Q2FW12
- Every structure of UniProt Q2FXK6
- Every structure of UniProt Q2FW23
- Every structure of UniProt Q2G113
- Every structure of UniProt P48940
- Every structure of UniProt Q2FW20
- Every structure of UniProt Q2FW39
- Every structure of UniProt Q931G5
- Every structure of UniProt Q2FW31
- Every structure of UniProt P0A0H0
- Every structure of UniProt Q2FW30
- Every structure of UniProt Q2FW19
- Every structure of UniProt Q2G2Q1
- Every structure of UniProt Q2FZ45
- Every structure of UniProt Q2FW15
- Every structure of UniProt Q2G111
- Every structure of UniProt Q2FW10
- Every structure of UniProt Q2FXY6
- Every structure of UniProt Q2G2Q4
- Elsewhere: RCSB PDB 8BYV · PDBe 8BYV · UniProt Q2FZ25 · UniProt Q2FW12 · UniProt Q2FXK6 · UniProt Q2FW23 · UniProt Q2G113 · UniProt P48940 · UniProt Q2FW20 · UniProt Q2FW39 · UniProt Q931G5 · UniProt Q2FW31 · UniProt P0A0H0 · UniProt Q2FW30 · UniProt Q2FW19 · UniProt Q2G2Q1 · UniProt Q2FZ45 · UniProt Q2FW15 · UniProt Q2G111 · UniProt Q2FW10 · UniProt Q2FXY6 · UniProt Q2G2Q4
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