MolNFT v1 · #85918 · protein + RNA
Structure of ribosome-apramycin complexes
4AQY · 16S ribosomal RNA: “Structure of ribosome-apramycin complexes”. X-ray diffraction, 4 ligands (AM2, MG, K), 20 pockets (best druggability 0.89). MolNFT v1 #85918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AQY
- Type
- protein + RNA
- Length
- 3,927 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
- P80373, P27152, P23370, P17291, P24319, P80375, P17293, P24320, P80378, P80379, P24321, P80381, P32193
- Ligands
- AM2, MG, K, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 23 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1510 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 38% helix, 10% strand | — |
| C | 30S ribosomal protein S3 | protein | 206 | 28% helix, 14% strand | — |
| D | 30S ribosomal protein S4 | protein | 208 | 37% helix, 8% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 29% helix, 37% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 28% helix, 27% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 54% helix, 9% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 25% helix, 25% strand | P24319 |
| I | 30S ribosomal protein S9 | protein | 127 | 28% helix, 19% strand | — |
| J | 30S ribosomal protein S10 | protein | 98 | 4% helix, 29% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 29% helix, 25% strand | — |
| L | 30S ribosomal protein S12 | protein | 124 | 5% helix, 27% strand | P17293 |
| M | 30S ribosomal protein S13 | protein | 125 | 47% helix, 2% strand | — |
| N | 30S ribosomal protein S14 | protein | 60 | 27% helix, 3% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 73% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 22% helix, 25% strand | P80379 |
| Q | 30S ribosomal protein S17 | protein | 104 | 13% helix, 45% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 73 | 34% helix, 8% strand | — |
| S | 30S ribosomal protein S19 | protein | 80 | 20% helix, 9% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 70% helix, 0% strand | — |
| V | 30S ribosomal protein thx | protein | 24 | 25% helix, 8% strand | P32193 |
| W | 5'-R(*UP*UP*CP*AP*AP*AP)-3' | rna | 6 | — | — |
| Z | 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3' | rna | 15 | — | — |
Ligands and binding sites
- AM2 · Apramycin · ligand · 5 copies · chains A, L
- MG · Magnesium ion · metal · 203 copies · chains A, N, T, D, V, L, Q, J, P, M, S, B, O, E, Z, F, G, I, H, K, W
- K · Potassium ion · metal · 15 copies · chains A, L, V
- 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 | 1084 | 0.89 | 0.92 | 87 | MG |
| 2 | 1095 | 0.85 | 0.87 | 117 | MG |
| 3 | 870 | 0.85 | 0.87 | 78 | MG |
| 4 | 937 | 0.85 | 0.87 | 81 | MG |
| 5 | 610 | 0.84 | 0.89 | 65 | K, MG |
Interfaces
48 interfaces between chains.
- A–L · 3382 Ų buried · 88 hydrogen bonds · protein-nucleic
- A–I · 3022 Ų buried · 104 hydrogen bonds · protein-nucleic
- A–Q · 2935 Ų buried · 58 hydrogen bonds · protein-nucleic
- A–D · 2914 Ų buried · 82 hydrogen bonds · protein-nucleic
- A–T · 2594 Ų buried · 65 hydrogen bonds · protein-nucleic
Compared structures
- 4AQY · Structure of ribosome-apramycin complexes · 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 P80373
- Every structure of UniProt P27152
- Every structure of UniProt P23370
- Every structure of UniProt P17291
- Every structure of UniProt P24319
- Every structure of UniProt P80375
- Every structure of UniProt P17293
- Every structure of UniProt P24320
- Every structure of UniProt P80378
- Every structure of UniProt P80379
- Every structure of UniProt P24321
- Every structure of UniProt P80381
- Every structure of UniProt P32193
- Elsewhere: RCSB PDB 4AQY · PDBe 4AQY · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80375 · UniProt P17293 · UniProt P24320 · UniProt P80378 · UniProt P80379 · UniProt P24321 · UniProt P80381 · UniProt P32193
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