MolNFT v1 · #182978 · protein + RNA
Bacterial 30S ribosomal subunit assembly complex state C (consensus refinement)
7NAU · 16S rRNA: “Bacterial 30S ribosomal subunit assembly complex state C (consensus refinement)”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #182978 on GenesisL1: 3D structure, binding sites…
- PDB
- 7NAU
- Type
- protein + RNA
- Length
- 4,012 residues
- Chains
- 21
- 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, P0A8A8
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 21 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1522 | — | — |
| B | 30S ribosomal protein S2 | protein | 224 | 50% helix, 14% strand | P0A7V0 |
| C | 30S ribosomal protein S3 | protein | 211 | 36% helix, 27% strand | P0A7V3 |
| D | 30S ribosomal protein S4 | protein | 205 | 44% helix, 8% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 156 | 30% helix, 34% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 106 | 35% helix, 34% strand | P02358 |
| G | 30S ribosomal protein S7 | protein | 146 | 57% helix, 5% strand | P02359 |
| H | 30S ribosomal protein S8 | protein | 129 | 29% helix, 30% strand | P0A7W7 |
| I | 30S ribosomal protein S9 | protein | 127 | 35% helix, 21% strand | P0A7X3 |
| J | 30S ribosomal protein S10 | protein | 99 | 25% helix, 38% strand | P0A7R5 |
| K | 30S ribosomal protein S11 | protein | 116 | 31% helix, 25% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 10% helix, 26% strand | P0A7S3 |
| M | 30S ribosomal protein S13 | protein | 114 | 51% helix, 2% strand | P0A7S9 |
| N | 30S ribosomal protein S14 | protein | 100 | 49% helix, 4% strand | P0AG59 |
| O | 30S ribosomal protein S15 | protein | 88 | 73% 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, 51% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 65 | 48% helix, 6% strand | P0A7T7 |
| S | 30S ribosomal protein S19 | protein | 82 | 23% helix, 18% strand | P0A7U3 |
| T | 30S ribosomal protein S20 | protein | 86 | 85% helix, 0% strand | P0A7U7 |
| X | Ribosome maturation factor rimp | protein | 151 | 25% helix, 31% 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 | 913 | 0.85 | 0.88 | 64 | MG |
| 2 | 744 | 0.84 | 0.88 | 74 | MG |
| 3 | 1190 | 0.84 | 0.85 | 98 | empty |
| 4 | 859 | 0.83 | 0.86 | 75 | MG |
| 5 | 497 | 0.80 | 0.88 | 55 | empty |
Interfaces
38 interfaces between chains.
- A–D · 3203 Ų buried · 90 hydrogen bonds · protein-nucleic
- A–I · 2909 Ų buried · 108 hydrogen bonds · protein-nucleic
- A–L · 2564 Ų buried · 77 hydrogen bonds · protein-nucleic
- A–T · 2197 Ų buried · 60 hydrogen bonds · protein-nucleic
- A–N · 2166 Ų buried · 66 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 modified (nucleotide modification, nonstandard).
Compared structures
- 7NAU · Bacterial 30S ribosomal subunit assembly complex state C (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 P0A8A8
- Elsewhere: RCSB PDB 7NAU · PDBe 7NAU · 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 P0A8A8
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