MolNFT v1 · #95373 · protein + RNA
Crystal structure of compound 4D bound to large ribosomal subunit (50S) from deinococcus radiodurans
4IO9 · 23S ribosomal RNA: “Crystal structure of compound 4D bound to large ribosomal subunit (50S) from deinococcus radiodurans”. X-ray diffraction, 2 ligands (1F2, MG), 20 pockets (best druggability 0.88). MolNFT v1 #95373 on GenesisL1…
- PDB
- 4IO9
- Type
- protein + RNA
- Length
- 5,997 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
- UniProt
- Q9RXJ9, Q9RXK2, Q9RXK1, Q9RXJ0, Q9RSL3, Q9RSS7, Q9RXY1, Q9RXJ2, Q9RSK9, Q9RXJ5, Q9RSJ5, Q9RSL2, Q9RWB4, Q9RSW7, Q9RY64, Q9RXJ7, Q9RXK0, Q9RXJ1, Q9RX88, Q9RY65, Q9RRG8, Q9RXJ4, Q9RSL0, P49228, Q9RSS4, Q9RSH2, Q9RSW6, Q9RSK0
- Ligands
- 1F2, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 30 distinct chains · 21% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 23S ribosomal RNA | rna | 2686 | — | — |
| Y | 5S ribosomal RNA | rna | 122 | — | — |
| A | 50S ribosomal protein L2 | protein | 240 | 5% helix, 23% strand | Q9RXJ9 |
| B | 50S ribosomal protein L3 | protein | 205 | 7% helix, 36% strand | Q9RXK2 |
| C | 50S ribosomal protein L4 | protein | 197 | 26% helix, 6% strand | Q9RXK1 |
| D | 50S ribosomal protein L5 | protein | 177 | 28% helix, 20% strand | Q9RXJ0 |
| E | 50S ribosomal protein L6 | protein | 171 | 20% helix, 32% strand | Q9RSL3 |
| F | 50S ribosomal protein L11 | protein | 71 | 39% helix, 6% strand | Q9RSS7 |
| G | 50S ribosomal protein L13 | protein | 142 | 27% helix, 15% strand | Q9RXY1 |
| H | 50S ribosomal protein L14 | protein | 134 | 7% helix, 36% strand | Q9RXJ2 |
| I | 50S ribosomal protein L15 | protein | 141 | 13% helix, 8% strand | Q9RSK9 |
| J | 50S ribosomal protein L16 | protein | 136 | 20% helix, 22% strand | Q9RXJ5 |
| K | 50S ribosomal protein L17 | protein | 113 | 50% helix, 16% strand | Q9RSJ5 |
| L | 50S ribosomal protein L18 | protein | 104 | 37% helix, 11% strand | Q9RSL2 |
| M | 50S ribosomal protein L19 | protein | 108 | 16% helix, 35% strand | Q9RWB4 |
| N | 50S ribosomal protein L20 | protein | 117 | 75% helix, 0% strand | Q9RSW7 |
| O | 50S ribosomal protein L21 | protein | 94 | 0% helix, 46% strand | Q9RY64 |
| P | 50S ribosomal protein L22 | protein | 127 | 40% helix, 31% strand | Q9RXJ7 |
| Q | 50S ribosomal protein L23 | protein | 93 | 19% helix, 31% strand | Q9RXK0 |
| R | 50S ribosomal protein L24 | protein | 110 | 0% helix, 26% strand | Q9RXJ1 |
| S | 50S ribosomal protein L25 | protein | 175 | 9% helix, 37% strand | Q9RX88 |
| T | 50S ribosomal protein L27 | protein | 84 | 0% helix, 36% strand | Q9RY65 |
| U | 50S ribosomal protein L28 | protein | 72 | 10% helix, 6% strand | Q9RRG8 |
| V | 50S ribosomal protein L29 | protein | 66 | 77% helix, 0% strand | Q9RXJ4 |
| W | 50S ribosomal protein L30 | protein | 55 | 38% helix, 18% strand | Q9RSL0 |
| Z | 50S ribosomal protein L32 | protein | 58 | 17% helix, 16% strand | P49228 |
| 1 | 50S ribosomal protein L33 | protein | 53 | 0% helix, 0% strand | Q9RSS4 |
| 2 | 50S ribosomal protein L34 | protein | 46 | 0% helix, 0% strand | Q9RSH2 |
| 3 | 50S ribosomal protein L35 | protein | 63 | 0% helix, 0% strand | Q9RSW6 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 8% helix, 22% strand | Q9RSK0 |
Ligands and binding sites
- 1F2 · (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate · ligand · chains X, P, Z
- MG · Magnesium ion · metal · 35 copies · chains X, B, C, Y, J, M
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 | 1038 | 0.88 | 0.91 | 98 | MG |
| 2 | 731 | 0.88 | 0.93 | 71 | empty |
| 3 | 928 | 0.87 | 0.90 | 85 | MG |
| 4 | 1181 | 0.87 | 0.89 | 115 | MG |
| 5 | 1165 | 0.86 | 0.88 | 111 | MG |
Interfaces
59 interfaces between chains.
- X–A · 6123 Ų buried · 156 hydrogen bonds · protein-nucleic
- X–B · 5139 Ų buried · 132 hydrogen bonds · protein-nucleic
- X–C · 4380 Ų buried · 98 hydrogen bonds · protein-nucleic
- X–N · 4250 Ų buried · 102 hydrogen bonds · protein-nucleic
- X–I · 4177 Ų buried · 82 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4IO9 · Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus… · the same entry in another collection · chain G against G, 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 Q9RXJ9
- Every structure of UniProt Q9RXK2
- Every structure of UniProt Q9RXK1
- Every structure of UniProt Q9RXJ0
- Every structure of UniProt Q9RSL3
- Every structure of UniProt Q9RSS7
- Every structure of UniProt Q9RXY1
- Every structure of UniProt Q9RXJ2
- Every structure of UniProt Q9RSK9
- Every structure of UniProt Q9RXJ5
- Every structure of UniProt Q9RSJ5
- Every structure of UniProt Q9RSL2
- Every structure of UniProt Q9RWB4
- Every structure of UniProt Q9RSW7
- Every structure of UniProt Q9RY64
- Every structure of UniProt Q9RXJ7
- Every structure of UniProt Q9RXK0
- Every structure of UniProt Q9RXJ1
- Every structure of UniProt Q9RX88
- Every structure of UniProt Q9RY65
- Every structure of UniProt Q9RRG8
- Every structure of UniProt Q9RXJ4
- Every structure of UniProt Q9RSL0
- Every structure of UniProt P49228
- Every structure of UniProt Q9RSS4
- Every structure of UniProt Q9RSH2
- Every structure of UniProt Q9RSW6
- Every structure of UniProt Q9RSK0
- Elsewhere: RCSB PDB 4IO9 · PDBe 4IO9 · UniProt Q9RXJ9 · UniProt Q9RXK2 · UniProt Q9RXK1 · UniProt Q9RXJ0 · UniProt Q9RSL3 · UniProt Q9RSS7 · UniProt Q9RXY1 · UniProt Q9RXJ2 · UniProt Q9RSK9 · UniProt Q9RXJ5 · UniProt Q9RSJ5 · UniProt Q9RSL2 · UniProt Q9RWB4 · UniProt Q9RSW7 · UniProt Q9RY64 · UniProt Q9RXJ7 · UniProt Q9RXK0 · UniProt Q9RXJ1 · UniProt Q9RX88 · UniProt Q9RY65 · UniProt Q9RRG8 · UniProt Q9RXJ4 · UniProt Q9RSL0 · UniProt P49228 · UniProt Q9RSS4 · UniProt Q9RSH2 · UniProt Q9RSW6 · UniProt Q9RSK0
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