MolNFT v1 · #160173 · protein + RNA
E. COLI 50S ribosome bound to compound 40O
6PCR · 23S ribosomal RNA: “E. COLI 50S ribosome bound to compound 40O”. Electron microscopy, 1 ligand (O8P), 20 pockets (best druggability 0.88). MolNFT v1 #160173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PCR
- Type
- protein + RNA
- Length
- 3,982 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
- O8P
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 18% helix, 23% 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 | 271 | 5% helix, 28% strand | P60422 |
| L | 50S ribosomal protein L15 | protein | 144 | 17% helix, 11% strand | A0A037Y8L6 |
| M | 50S ribosomal protein L4 | protein | 201 | 34% helix, 12% strand | D7Z9F6 |
| N | 50S ribosomal protein L3 | protein | 209 | 8% helix, 37% strand | P60438 |
| O | 50S ribosomal protein L13 | protein | 142 | 34% helix, 18% strand | D7ZET0 |
Ligands and binding sites
- O8P · (2R)-2-[(3s,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-1,7,16,22-tetraoxo-4,7,8,9,14,15,16,17,24,25, 26,26A-dodecahydro-1H,3H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl (2-bromopyridin-4-yl)carbamate · 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 | 971 | 0.88 | 0.91 | 103 | empty |
| 2 | 867 | 0.87 | 0.90 | 81 | empty |
| 3 | 740 | 0.86 | 0.90 | 87 | empty |
| 4 | 1093 | 0.86 | 0.88 | 110 | empty |
| 5 | 823 | 0.86 | 0.89 | 86 | empty |
Interfaces
8 interfaces between chains.
- I–K · 7249 Ų buried · 188 hydrogen bonds · protein-nucleic
- I–N · 5083 Ų buried · 113 hydrogen bonds · protein-nucleic
- I–L · 4499 Ų buried · 107 hydrogen bonds · protein-nucleic
- I–M · 4192 Ų buried · 95 hydrogen bonds · protein-nucleic
- I–O · 2722 Ų buried · 58 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 21 modified (nucleotide modification).
Compared structures
- 6PCR · E. coli 50S ribosome bound to compound 40o · the same entry in another collection · chain I against I, 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 6PCR · PDBe 6PCR · UniProt P60422 · UniProt A0A037Y8L6 · UniProt D7Z9F6 · UniProt P60438 · UniProt D7ZET0
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