MolNFT v1 · #65152 · protein
HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor (R)- 11D
3GOL · RNA-directed RNA polymerase: “HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor (R)- 11D”. X-ray diffraction, 2 ligands (XND, MG), 13 pockets (best druggability 0.80). MolNFT v1 #65152 on GenesisL1: 3D structure…
- PDB
- 3GOL
- Type
- protein
- Length
- 1,116 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- O92972
- Ligands
- XND, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 49% helix, 15% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 559 | 49% helix, 15% strand | O92972 |
Ligands and binding sites
- XND · (11R)-10-acetyl-11-(2,4-dichlorophenyl)-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.80 | 0.82 | 84 | XND, MG |
| 2 | 994 | 0.80 | 0.81 | 76 | XND, MG |
| 3 | 1130 | 0.72 | 0.76 | 100 | empty |
| 4 | 90 | 0.54 | 0.85 | 16 | empty |
| 5 | 114 | 0.46 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 266 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3GOL · HCV NS5b polymerase in complex with 1,5 benzodiazepine inhibitor (R)-11d · the same entry in another collection · chain A against A, 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 O92972
- Elsewhere: RCSB PDB 3GOL · PDBe 3GOL · UniProt O92972
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