Research workbench
Crystal structure of HCV NS5B polymerase with compound 2
Analyse Crystal structure of HCV NS5B polymerase with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JTY
- Type
- protein
- Length
- 1,120 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
- 1NV, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 560 | 49% helix, 14% strand | O92972 |
Ligands and binding sites
- 1NV · 3-{[4-oxo-1-(2,4,6-trifluorobenzyl)-1,4-dihydroquinazolin-6-yl]oxy}-2-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.81 | 0.82 | 87 | GOL |
| 2 | 1000 | 0.80 | 0.82 | 75 | GOL |
| 3 | 137 | 0.50 | 0.79 | 18 | empty |
| 4 | 151 | 0.47 | 0.77 | 22 | 1NV |
| 5 | 119 | 0.47 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 969 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4JTY · Crystal structure of HCV NS5B polymerase with COMPOUND 2 · 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 4JTY · PDBe 4JTY · UniProt O92972
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.