Research workbench
Crystal structure of the 30S ribosome in complex with compound 37
Analyse Crystal structure of the 30S ribosome in complex with compound 37 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B3S
- Type
- protein + RNA
- Length
- 3,925 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- RPO, MG, K, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 23 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1510 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 40% helix, 13% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 35% helix, 19% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 39% helix, 8% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 29% helix, 38% strand | Q5SHQ5 |
| F | 30S ribosomal protein S6 | protein | 101 | 29% helix, 36% strand | Q5SLP8 |
| G | 30S ribosomal protein S7 | protein | 155 | 52% helix, 10% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 25% helix, 22% strand | Q5SHQ2 |
| I | 30S ribosomal protein S9 | protein | 127 | 26% helix, 19% strand | P80374 |
| J | 30S ribosomal protein S10 | protein | 98 | 15% helix, 23% strand | Q5SHN7 |
| K | 30S ribosomal protein S11 | protein | 119 | 24% helix, 24% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 124 | 6% helix, 27% strand | Q5SHN3 |
| M | 30S ribosomal protein S13 | protein | 125 | 44% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 type Z | protein | 60 | 27% helix, 10% strand | Q5SHQ1 |
| O | 30S ribosomal protein S15 | protein | 88 | 73% helix, 0% strand | Q5SJ76 |
| P | 30S ribosomal protein S16 | protein | 83 | 23% helix, 36% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 104 | 13% helix, 46% strand | Q5SHP7 |
| R | 30S ribosomal protein S18 | protein | 73 | 37% helix, 7% strand | Q5SLQ0 |
| S | 30S ribosomal protein S19 | protein | 80 | 21% helix, 9% strand | Q5SHP2 |
| T | 30S ribosomal protein S20 | protein | 99 | 69% helix, 0% strand | P80380 |
| V | 30S ribosomal protein thx | protein | 24 | 29% helix, 8% strand | Q5SIH3 |
| W | 5'-R(*UP*UP*CP*AP*AP*AP)-3' | rna | 4 | — | — |
| Z | 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3' | rna | 15 | — | — |
Ligands and binding sites
- RPO · (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranoside · ligand · chains A, L
- MG · Magnesium ion · metal · 166 copies · chains A, E, N, K, V, L, W, Q, J, S, T, M, G, B, F, H
- K · Potassium ion · metal · 13 copies · chains A, L, M
- ZN · Zinc ion · metal · 2 copies · chains D, N
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 | 1051 | 0.89 | 0.91 | 94 | MG |
| 2 | 1014 | 0.85 | 0.86 | 115 | MG |
| 3 | 594 | 0.84 | 0.90 | 66 | MG |
| 4 | 558 | 0.84 | 0.90 | 91 | empty |
| 5 | 1059 | 0.84 | 0.85 | 84 | MG, K |
Interfaces
45 interfaces between chains.
- A–L · 3356 Ų buried · 92 hydrogen bonds · protein-nucleic
- A–I · 3088 Ų buried · 100 hydrogen bonds · protein-nucleic
- A–D · 2964 Ų buried · 91 hydrogen bonds · protein-nucleic
- A–Q · 2908 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–T · 2598 Ų buried · 68 hydrogen bonds · protein-nucleic
Compared structures
- 4B3S · Crystal structure of the 30S ribosome in complex with compound 37 · the same entry in another collection · chain K against K, 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 P80371
- Every structure of UniProt P80372
- Every structure of UniProt P80373
- Every structure of UniProt Q5SHQ5
- Every structure of UniProt Q5SLP8
- Every structure of UniProt P17291
- Every structure of UniProt Q5SHQ2
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt Q5SHN3
- Every structure of UniProt P80377
- Every structure of UniProt Q5SHQ1
- Every structure of UniProt Q5SJ76
- Every structure of UniProt Q5SJH3
- Every structure of UniProt Q5SHP7
- Every structure of UniProt Q5SLQ0
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P80380
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 4B3S · PDBe 4B3S · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt Q5SHN3 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt Q5SHP7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3
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