MolNFT v1 · #174215 · protein + RNA
Bacterial 30S ribosomal subunit assembly complex state F (multibody refinement for body domain of 30S ribosome)
7BOI · 16S rRNA: “Bacterial 30S ribosomal subunit assembly complex state F (multibody refinement for body domain of 30S…”. Electron microscopy, 3 ligands (GNP, MG, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #174215 on GenesisL1…
- PDB
- 7BOI
- Type
- protein + RNA
- Length
- 2,695 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S4; 30S ribosomal protein S5; 30S ribosomal protein S6…
- EC
- 3.6.1.-
- UniProt
- P0A7V8, P0A7W1, P02358, P0A7W7, P0A7R9, P0A7S3, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U7, P68679, P39286
- Ligands
- GNP, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 14 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1078 | — | — |
| D | 30S ribosomal protein S4 | protein | 205 | 42% helix, 9% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 156 | 30% helix, 37% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 106 | 26% helix, 28% strand | P02358 |
| H | 30S ribosomal protein S8 | protein | 129 | 29% helix, 33% strand | P0A7W7 |
| K | 30S ribosomal protein S11 | protein | 117 | 23% helix, 29% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 11% helix, 28% strand | P0A7S3 |
| O | 30S ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | P0ADZ4 |
| P | 30S ribosomal protein S16 | protein | 82 | 26% helix, 33% strand | P0A7T3 |
| Q | 30S ribosomal protein S17 | protein | 80 | 4% helix, 61% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 65 | 43% helix, 3% strand | P0A7T7 |
| T | 30S ribosomal protein S20 | protein | 86 | 86% helix, 0% strand | P0A7U7 |
| U | 30S ribosomal protein S21 | protein | 66 | 68% helix, 3% strand | P68679 |
| W | Small ribosomal subunit biogenesis GTPase rsga (EC 3.6.1.-) | protein | 314 | 26% helix, 29% strand | P39286 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains W
- MG · Magnesium ion · metal · 72 copies · chains A, E, L, T, Q, O, W
- ZN · Zinc ion · metal · chains W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 698 | 0.83 | 0.88 | 63 | MG |
| 2 | 1117 | 0.83 | 0.85 | 90 | MG |
| 3 | 1176 | 0.82 | 0.84 | 85 | MG |
| 4 | 901 | 0.82 | 0.85 | 85 | MG |
| 5 | 861 | 0.81 | 0.84 | 69 | MG |
Interfaces
23 interfaces between chains.
- A–L · 3319 Ų buried · 91 hydrogen bonds · protein-nucleic
- A–D · 3242 Ų buried · 88 hydrogen bonds · protein-nucleic
- A–T · 2383 Ų buried · 53 hydrogen bonds · protein-nucleic
- A–P · 2157 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–W · 1958 Ų buried · 44 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 modified (nucleotide modification, nonstandard).
Compared structures
- 7BOI · Bacterial 30S ribosomal subunit assembly complex state F (multibody refinement for body… · the same entry in another collection · chain W against W, TM-score 1.00
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 P0A7V8
- Every structure of UniProt P0A7W1
- Every structure of UniProt P02358
- Every structure of UniProt P0A7W7
- Every structure of UniProt P0A7R9
- Every structure of UniProt P0A7S3
- Every structure of UniProt P0ADZ4
- Every structure of UniProt P0A7T3
- Every structure of UniProt P0AG63
- Every structure of UniProt P0A7T7
- Every structure of UniProt P0A7U7
- Every structure of UniProt P68679
- Every structure of UniProt P39286
- Elsewhere: RCSB PDB 7BOI · PDBe 7BOI · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P0A7W7 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U7 · UniProt P68679 · UniProt P39286
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