Research workbench
HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 1B
Analyse HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GNV
- 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
- XNZ
- Pockets
- 16 · 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 | 563 | 49% helix, 15% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 553 | 49% helix, 15% strand | O92972 |
Ligands and binding sites
- XNZ · (11R)-10-acetyl-11-[4-(benzyloxy)-2-chlorophenyl]-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
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.80 | 0.81 | 88 | XNZ |
| 2 | 1049 | 0.80 | 0.81 | 84 | XNZ |
| 3 | 708 | 0.72 | 0.79 | 56 | empty |
| 4 | 138 | 0.48 | 0.78 | 20 | empty |
| 5 | 95 | 0.44 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 425 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3GNV · HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 1b · 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 3GNV · PDBe 3GNV · UniProt O92972
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