MolNFT v1 · #36411 · protein + RNA
30S ribosome + designer antibiotic
2F4V · 16S ribosomal RNA: “30S ribosome + designer antibiotic”. X-ray diffraction, 5 ligands (D2C, AB9, MG), 20 pockets (best druggability 0.85). MolNFT v1 #36411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2F4V
- Type
- protein + RNA
- Length
- 3,891 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 5'-R(P*UP*UP*CP*U)-3'; 30S ribosomal protein S2; 30S ribosomal protein…
- UniProt
- P80371, P80372, P80373, P27152, P23370, P17291, P24319, P62669, P80375, P80376, P17293, P80377, P24320, P80378, Q5SJH3, P24321, P80382, P80381, P62661
- Ligands
- D2C, AB9, MG, K, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 21 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1507 | — | — |
| Z | 5'-R(P*UP*UP*CP*U)-3' | rna | 4 | — | — |
| B | 30S ribosomal protein S2 | protein | 237 | 38% helix, 6% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 31% helix, 16% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 39% helix, 7% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 29% helix, 37% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 24% helix, 36% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 50% helix, 10% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 24% helix, 30% strand | P24319 |
| I | 30S ribosomal protein S9 | protein | 127 | 24% helix, 18% strand | P62669 |
| J | 30S ribosomal protein S10 | protein | 98 | 12% helix, 21% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 24% helix, 27% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 125 | 5% helix, 17% strand | P17293 |
| M | 30S ribosomal protein S13 | protein | 125 | 48% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 | protein | 60 | 22% helix, 5% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 70% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 20% helix, 27% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 104 | 12% helix, 42% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 73 | 38% helix, 8% strand | P80382 |
| S | 30S ribosomal protein S19 | protein | 84 | 15% helix, 15% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 69% helix, 0% strand | P62661 |
Ligands and binding sites
- D2C · (2s,4s,4ar,5as,6s,11r,11as,12r,12ar)-7-chloro-4-(dimethylamino)-6,10,11,12-tetrahydroxy-1,3-dioxo-1,2,3,4,4A,5,5A,6,11,11A,12,12A-dodecahydrotetracene-2-carboxamide · ligand · chains A
- AB9 · (2R)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-2-{2-[(2-aminoethyl)amino]ethoxy}-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide · ligand · chains A, Z
- MG · Magnesium ion · metal · 101 copies · chains A, E, C, D, L, T, Z, J, M, P
- K · Potassium ion · metal · 12 copies · chains A, N
- ZN · Zinc ion · metal · 2 copies · chains D, A, 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 | 1067 | 0.85 | 0.87 | 106 | MG |
| 2 | 1168 | 0.85 | 0.87 | 85 | MG |
| 3 | 883 | 0.84 | 0.87 | 81 | MG |
| 4 | 900 | 0.84 | 0.87 | 77 | MG, K |
| 5 | 677 | 0.84 | 0.89 | 71 | MG |
Interfaces
40 interfaces between chains.
- A–L · 3293 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–I · 3156 Ų buried · 93 hydrogen bonds · protein-nucleic
- A–D · 3122 Ų buried · 81 hydrogen bonds · protein-nucleic
- A–Q · 2899 Ų buried · 63 hydrogen bonds · protein-nucleic
- A–P · 2592 Ų buried · 49 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2F4V · 30S ribosome + designer antibiotic · the same entry in another collection · chain J against J, 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 P27152
- Every structure of UniProt P23370
- Every structure of UniProt P17291
- Every structure of UniProt P24319
- Every structure of UniProt P62669
- Every structure of UniProt P80375
- Every structure of UniProt P80376
- Every structure of UniProt P17293
- Every structure of UniProt P80377
- Every structure of UniProt P24320
- Every structure of UniProt P80378
- Every structure of UniProt Q5SJH3
- Every structure of UniProt P24321
- Every structure of UniProt P80382
- Every structure of UniProt P80381
- Every structure of UniProt P62661
- Elsewhere: RCSB PDB 2F4V · PDBe 2F4V · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P62669 · UniProt P80375 · UniProt P80376 · UniProt P17293 · UniProt P80377 · UniProt P24320 · UniProt P80378 · UniProt Q5SJH3 · UniProt P24321 · UniProt P80382 · UniProt P80381 · UniProt P62661
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