Research workbench
Bacterial 30S ribosomal subunit assembly complex state I (body domain)
Analyse Bacterial 30S ribosomal subunit assembly complex state I (body domain) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BOF
- Type
- protein + RNA
- Length
- 2,308 residues
- Chains
- 12
- 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…
- UniProt
- P0A7V8, P0A7W1, P02358, P0A7W7, P0A7R9, P0A7S3, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 12 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1070 | — | — |
| D | 30S ribosomal protein S4 | protein | 205 | 42% helix, 10% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 157 | 31% helix, 36% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 106 | 28% helix, 30% strand | P02358 |
| H | 30S ribosomal protein S8 | protein | 129 | 26% helix, 32% strand | P0A7W7 |
| K | 30S ribosomal protein S11 | protein | 117 | 28% helix, 27% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 11% helix, 28% strand | P0A7S3 |
| O | 30S ribosomal protein S15 | protein | 88 | 76% helix, 0% strand | P0ADZ4 |
| P | 30S ribosomal protein S16 | protein | 82 | 26% helix, 38% strand | P0A7T3 |
| Q | 30S ribosomal protein S17 | protein | 80 | 4% helix, 58% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 65 | 48% helix, 3% strand | P0A7T7 |
| T | 30S ribosomal protein S20 | protein | 86 | 84% helix, 0% strand | P0A7U7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 129 copies · chains A, Q, E, K, D
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 | 1181 | 0.83 | 0.85 | 88 | MG |
| 2 | 445 | 0.82 | 0.90 | 56 | MG |
| 3 | 293 | 0.81 | 0.93 | 42 | MG |
| 4 | 832 | 0.81 | 0.84 | 76 | MG |
| 5 | 550 | 0.79 | 0.86 | 45 | MG |
Interfaces
18 interfaces between chains.
- A–D · 3380 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–L · 2897 Ų buried · 81 hydrogen bonds · protein-nucleic
- A–T · 2359 Ų buried · 48 hydrogen bonds · protein-nucleic
- A–P · 2101 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–K · 1880 Ų buried · 44 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification, nonstandard).
Compared structures
- 7BOF · Bacterial 30S ribosomal subunit assembly complex state I (body domain) · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 7BOF · PDBe 7BOF · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P0A7W7 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U7
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