Research workbench
E. COLI 50S ribosome bound to VM2
Analyse E. COLI 50S ribosome bound to VM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PCQ
- 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
- O8J
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 18% helix, 21% 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 | 5% helix, 27% strand | P60422 |
| L | 50S ribosomal protein L15 | protein | 144 | 17% helix, 9% strand | A0A037Y8L6 |
| M | 50S ribosomal protein L4 | protein | 201 | 34% helix, 10% strand | D7Z9F6 |
| N | 50S ribosomal protein L3 | protein | 206 | 9% helix, 37% strand | P60438 |
| O | 50S ribosomal protein L13 | protein | 142 | 35% helix, 18% strand | D7ZET0 |
Ligands and binding sites
- O8J · (3r,4r,5e,10e,12e,14s,26ar)-14-hydroxy-4,12-dimethyl-3-(propan-2-yl)-8,9,14,15,24,25,26,26A-octahydro-1H,3H, 22H-21,18-(azeno)pyrrolo[2,1-C][1,8,4, 19]dioxadiazacyclotetracosine-1,7,16,22(4H,17H)-tetrone · 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 | 1156 | 0.88 | 0.91 | 110 | empty |
| 2 | 1110 | 0.88 | 0.90 | 108 | empty |
| 3 | 967 | 0.87 | 0.89 | 89 | empty |
| 4 | 728 | 0.86 | 0.90 | 95 | empty |
| 5 | 964 | 0.85 | 0.87 | 66 | empty |
Interfaces
8 interfaces between chains.
- I–K · 7129 Ų buried · 186 hydrogen bonds · protein-nucleic
- I–N · 4937 Ų buried · 107 hydrogen bonds · protein-nucleic
- I–L · 4554 Ų buried · 103 hydrogen bonds · protein-nucleic
- I–M · 4156 Ų buried · 84 hydrogen bonds · protein-nucleic
- I–O · 2755 Ų buried · 58 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 21 modified (nucleotide modification).
Compared structures
- 6PCQ · E. coli 50S ribosome bound to VM2 · 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 6PCQ · PDBe 6PCQ · UniProt P60422 · UniProt A0A037Y8L6 · UniProt D7Z9F6 · UniProt P60438 · UniProt D7ZET0
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