Research workbench
HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 4C
Analyse HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 4C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GNW
- Type
- protein
- Length
- 1,128 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
- XNC, CL
- Pockets
- 14 · best druggability 0.81
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 | 560 | 49% helix, 15% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 568 | 49% helix, 16% strand | O92972 |
Ligands and binding sites
- XNC · (11S)-11-[4-(benzyloxy)-2-fluorophenyl]-3,3-dimethyl-10-[(6-methylpyridin-2-yl)carbonyl]-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.81 | 0.82 | 87 | XNC, CL |
| 2 | 1081 | 0.80 | 0.82 | 81 | XNC, CL |
| 3 | 948 | 0.71 | 0.76 | 83 | empty |
| 4 | 135 | 0.47 | 0.77 | 19 | empty |
| 5 | 118 | 0.46 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 408 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3GNW · HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 4c · 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 3GNW · PDBe 3GNW · UniProt O92972
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