Research workbench
E. coli 50S ribosome bound to compound 40q
Analyse E. coli 50S ribosome bound to compound 40q in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PC8
- Type
- protein + RNA
- Length
- 3,982 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Escherichia coli
- Molecule
- 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L15…
- UniProt
- P60422, A0A037Y8L6, D7Z9F6, P60438, D7ZET0
- Ligands
- O7Y
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.9 · 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 | 271 | 4% helix, 26% strand | P60422 |
| L | 50S ribosomal protein L15 | protein | 144 | 18% helix, 5% strand | A0A037Y8L6 |
| M | 50S ribosomal protein L4 | protein | 201 | 34% helix, 11% strand | D7Z9F6 |
| N | 50S ribosomal protein L3 | protein | 209 | 9% helix, 37% strand | P60438 |
| O | 50S ribosomal protein L13 | protein | 142 | 35% helix, 18% strand | D7ZET0 |
Ligands and binding sites
- O7Y · (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 isoquinolin-3-ylcarbamate · 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 | 1119 | 0.88 | 0.91 | 109 | empty |
| 2 | 1082 | 0.88 | 0.90 | 101 | empty |
| 3 | 590 | 0.85 | 0.91 | 64 | empty |
| 4 | 566 | 0.85 | 0.91 | 74 | empty |
| 5 | 887 | 0.84 | 0.87 | 63 | empty |
Interfaces
8 interfaces between chains.
- I–K · 7181 Ų buried · 167 hydrogen bonds · protein-nucleic
- I–N · 5076 Ų buried · 120 hydrogen bonds · protein-nucleic
- I–L · 4508 Ų buried · 97 hydrogen bonds · protein-nucleic
- I–M · 4205 Ų buried · 91 hydrogen bonds · protein-nucleic
- I–O · 2748 Ų buried · 58 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 21 modified (nucleotide modification).
Compared structures
- 6PC8 · E. COLI 50S ribosome bound to compound 40Q · 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 6PC8 · PDBe 6PC8 · UniProt P60422 · UniProt A0A037Y8L6 · UniProt D7Z9F6 · UniProt P60438 · UniProt D7ZET0
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