MolNFT v1 · #128365 · protein + RNA
Rsga-gdpnp bound to the 30S ribosomal subunit (rsga assembly intermediate with US3)
5NO4 · 16S ribosomal RNA: “Rsga-gdpnp bound to the 30S ribosomal subunit (rsga assembly intermediate with US3)”. Electron microscopy, 3 ligands (GNP, MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #128365 on GenesisL1: 3D…
- PDB
- 5NO4
- Type
- protein + RNA
- Length
- 3,796 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal…
- EC
- 3.6.1.-
- UniProt
- P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P39286
- Ligands
- GNP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1534 | — | — |
| C | 30S ribosomal protein S3 | protein | 206 | 37% helix, 31% strand | P0A7V3 |
| D | 30S ribosomal protein S4 | protein | 205 | 37% helix, 9% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 155 | 26% helix, 32% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 106 | 34% helix, 36% strand | P02358 |
| G | 30S ribosomal protein S7 | protein | 107 | 62% helix, 0% strand | P02359 |
| H | 30S ribosomal protein S8 | protein | 129 | 26% helix, 31% strand | P0A7W7 |
| I | 30S ribosomal protein S9 | protein | 127 | 28% helix, 19% strand | P0A7X3 |
| J | 30S ribosomal protein S10 | protein | 99 | 24% helix, 44% strand | P0A7R5 |
| K | 30S ribosomal protein S11 | protein | 117 | 15% helix, 29% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 14 | 43% helix, 0% strand | P0A7S3 |
| M | 30S ribosomal protein S13 | protein | 114 | 51% helix, 2% strand | P0A7S9 |
| N | 30S ribosomal protein S14 | protein | 100 | 40% helix, 4% strand | P0AG59 |
| O | 30S ribosomal protein S15 | protein | 88 | 74% helix, 0% strand | P0ADZ4 |
| P | 30S ribosomal protein S16 | protein | 82 | 22% helix, 34% strand | P0A7T3 |
| Q | 30S ribosomal protein S17 | protein | 80 | 4% helix, 55% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 55 | 45% helix, 4% strand | P0A7T7 |
| S | 30S ribosomal protein S19 | protein | 79 | 28% helix, 19% strand | P0A7U3 |
| T | 30S ribosomal protein S20 | protein | 86 | 85% helix, 0% strand | P0A7U7 |
| Z | Small ribosomal subunit biogenesis GTPase rsga (EC 3.6.1.-) | protein | 313 | 24% helix, 23% strand | P39286 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Z
- MG · Magnesium ion · metal · 71 copies · chains A, D, T, E, N, M, P, Z
- ZN · Zinc ion · metal · chains Z
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 | 1150 | 0.86 | 0.87 | 117 | MG |
| 2 | 1103 | 0.85 | 0.86 | 79 | empty |
| 3 | 1024 | 0.84 | 0.85 | 88 | MG |
| 4 | 913 | 0.84 | 0.86 | 87 | MG |
| 5 | 711 | 0.83 | 0.88 | 69 | MG |
Interfaces
37 interfaces between chains.
- A–D · 3104 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–I · 2854 Ų buried · 58 hydrogen bonds · protein-nucleic
- A–T · 2379 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–Z · 2311 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–N · 2203 Ų buried · 40 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 11 modified (nucleotide modification).
Compared structures
- 5NO4 · RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate with uS3) · the same entry in another collection · chain Z against Z, 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 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 P39286
- Elsewhere: RCSB PDB 5NO4 · PDBe 5NO4 · 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 P39286
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