MolNFT v1 · #160155 · protein + RNA
E. COLI 50S ribosome bound to compound 47
6PC6 · 23S ribosomal RNA: “E. COLI 50S ribosome bound to compound 47”. Electron microscopy, 1 ligand (O7S), 20 pockets (best druggability 0.87). MolNFT v1 #160155 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PC6
- Type
- protein + RNA
- Length
- 3,978 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L15…
- UniProt
- P60422, A0A037Y8L6, D7Z9F6, P60438, D7ZET0
- Ligands
- O7S
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 18% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | 23S ribosomal RNA | rna | 2897 | — | — |
| J | 5S ribosomal RNA | rna | 118 | — | — |
| K | 50S ribosomal protein L2 | protein | 270 | 4% helix, 27% strand | P60422 |
| L | 50S ribosomal protein L15 | protein | 144 | 17% helix, 10% strand | A0A037Y8L6 |
| M | 50S ribosomal protein L4 | protein | 201 | 34% helix, 12% strand | D7Z9F6 |
| N | 50S ribosomal protein L3 | protein | 206 | 9% helix, 35% strand | P60438 |
| O | 50S ribosomal protein L13 | protein | 142 | 33% helix, 18% strand | D7ZET0 |
Ligands and binding sites
- O7S · (3r,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9, 14,15,16,17,24,25,26,26A-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-C][1,8,4, 19]dioxadiazacyclotetracosine-1,7,22-trione · ligand · chains I
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 | 902 | 0.87 | 0.90 | 85 | empty |
| 2 | 563 | 0.84 | 0.90 | 72 | empty |
| 3 | 919 | 0.84 | 0.87 | 68 | empty |
| 4 | 625 | 0.83 | 0.89 | 71 | empty |
| 5 | 454 | 0.83 | 0.91 | 49 | empty |
Interfaces
8 interfaces between chains.
- I–K · 7121 Ų buried · 189 hydrogen bonds · protein-nucleic
- I–N · 4900 Ų buried · 107 hydrogen bonds · protein-nucleic
- I–L · 4523 Ų buried · 95 hydrogen bonds · protein-nucleic
- I–M · 4172 Ų buried · 92 hydrogen bonds · protein-nucleic
- I–O · 2724 Ų buried · 60 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 21 modified (nucleotide modification).
Compared structures
- 6PC6 · E. coli 50S ribosome bound to compound 47 · 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 P60422
- Every structure of UniProt A0A037Y8L6
- Every structure of UniProt D7Z9F6
- Every structure of UniProt P60438
- Every structure of UniProt D7ZET0
- Elsewhere: RCSB PDB 6PC6 · PDBe 6PC6 · UniProt P60422 · UniProt A0A037Y8L6 · UniProt D7Z9F6 · UniProt P60438 · UniProt D7ZET0
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