Research workbench
Crystal structure of HCV NS5B polymerase in complex with compound 3
Analyse Crystal structure of HCV NS5B polymerase in complex with compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JY0
- Type
- protein
- Length
- 1,117 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
- UniProt
- O92972
- Ligands
- 1O9
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 559 | 47% helix, 15% strand | O92972 |
| B | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 558 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- 1O9 · (4S,5R)-1-(4-tert-butylbenzoyl)-2-(2-methylpropyl)-4-pyrazin-2-yl-5-(1,3-thiazol-2-yl)-L-proline · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.81 | 0.84 | 72 | 1O9 |
| 2 | 973 | 0.80 | 0.81 | 88 | 1O9 |
| 3 | 106 | 0.52 | 0.83 | 19 | empty |
| 4 | 144 | 0.47 | 0.77 | 17 | empty |
| 5 | 121 | 0.45 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1018 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4JY0 · Crystal structure of hcv ns5b polymerase in complex with compound 3 · 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 4JY0 · PDBe 4JY0 · UniProt O92972
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