Research workbench
Bacterial 30S ribosomal subunit assembly complex state D (consensus refinement)
Analyse Bacterial 30S ribosomal subunit assembly complex state D (consensus refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NAV
- Type
- protein + RNA
- Length
- 4,105 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
- UniProt
- P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P0A7G2, P0A8A8
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 22 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1510 | — | — |
| B | 30S ribosomal protein S2 | protein | 224 | 50% helix, 14% strand | P0A7V0 |
| C | 30S ribosomal protein S3 | protein | 211 | 33% helix, 27% strand | P0A7V3 |
| D | 30S ribosomal protein S4 | protein | 205 | 41% helix, 6% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 156 | 28% helix, 36% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 106 | 28% helix, 35% strand | P02358 |
| G | 30S ribosomal protein S7 | protein | 151 | 56% helix, 3% strand | P02359 |
| H | 30S ribosomal protein S8 | protein | 129 | 29% helix, 25% strand | P0A7W7 |
| I | 30S ribosomal protein S9 | protein | 127 | 35% helix, 21% strand | P0A7X3 |
| J | 30S ribosomal protein S10 | protein | 99 | 25% helix, 36% strand | P0A7R5 |
| K | 30S ribosomal protein S11 | protein | 117 | 30% helix, 20% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 11% helix, 28% strand | P0A7S3 |
| M | 30S ribosomal protein S13 | protein | 114 | 51% helix, 0% strand | P0A7S9 |
| N | 30S ribosomal protein S14 | protein | 100 | 49% helix, 2% strand | P0AG59 |
| O | 30S ribosomal protein S15 | protein | 88 | 73% helix, 0% strand | P0ADZ4 |
| P | 30S ribosomal protein S16 | protein | 82 | 26% helix, 28% strand | P0A7T3 |
| Q | 30S ribosomal protein S17 | protein | 80 | 4% helix, 58% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 65 | 46% helix, 3% strand | P0A7T7 |
| S | 30S ribosomal protein S19 | protein | 82 | 16% helix, 18% strand | P0A7U3 |
| T | 30S ribosomal protein S20 | protein | 86 | 87% helix, 0% strand | P0A7U7 |
| V | 30S ribosome-binding factor | protein | 99 | 43% helix, 17% strand | P0A7G2 |
| X | Ribosome maturation factor rimp | protein | 151 | 26% helix, 28% strand | P0A8A8 |
Ligands and binding sites
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 | 778 | 0.85 | 0.89 | 55 | MG |
| 2 | 724 | 0.84 | 0.89 | 72 | empty |
| 3 | 657 | 0.84 | 0.89 | 75 | empty |
| 4 | 990 | 0.83 | 0.85 | 81 | empty |
| 5 | 946 | 0.83 | 0.85 | 96 | empty |
Interfaces
41 interfaces between chains.
- A–D · 2979 Ų buried · 102 hydrogen bonds · protein-nucleic
- A–I · 2735 Ų buried · 107 hydrogen bonds · protein-nucleic
- A–L · 2547 Ų buried · 79 hydrogen bonds · protein-nucleic
- A–T · 2224 Ų buried · 72 hydrogen bonds · protein-nucleic
- A–N · 2199 Ų buried · 77 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 modified (nucleotide modification, nonstandard).
Compared structures
- 7NAV · Bacterial 30S ribosomal subunit assembly complex state D (Consensus refinement) · the same entry in another collection · chain X against X, 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 P0A7V0
- Every structure of UniProt P0A7V3
- Every structure of UniProt P0A7V8
- Every structure of UniProt P0A7W1
- Every structure of UniProt P02358
- Every structure of UniProt P02359
- Every structure of UniProt P0A7W7
- Every structure of UniProt P0A7X3
- Every structure of UniProt P0A7R5
- Every structure of UniProt P0A7R9
- Every structure of UniProt P0A7S3
- Every structure of UniProt P0A7S9
- Every structure of UniProt P0AG59
- Every structure of UniProt P0ADZ4
- Every structure of UniProt P0A7T3
- Every structure of UniProt P0AG63
- Every structure of UniProt P0A7T7
- Every structure of UniProt P0A7U3
- Every structure of UniProt P0A7U7
- Every structure of UniProt P0A7G2
- Every structure of UniProt P0A8A8
- Elsewhere: RCSB PDB 7NAV · PDBe 7NAV · UniProt P0A7V0 · UniProt P0A7V3 · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P02359 · UniProt P0A7W7 · UniProt P0A7X3 · UniProt P0A7R5 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0A7S9 · UniProt P0AG59 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U3 · UniProt P0A7U7 · UniProt P0A7G2 · UniProt P0A8A8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.