Research workbench
HCV NS5B 1A Y316 bound to compound 49
Analyse HCV NS5B 1A Y316 bound to compound 49 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MVO
- Type
- protein
- Length
- 1,124 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
- Q66N85
- Ligands
- K4P, SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 562 | 50% helix, 16% strand | Q66N85 |
Ligands and binding sites
- K4P · 6-[(7-chloro-1-hydroxy-1,3-dihydro-2,1-benzoxaborol-5-yl)(methylsulfonyl)amino]-5-cyclopropyl-2-(4-fluorophenyl)-N-methyl-1-benzofuran-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.82 | 0.83 | 99 | SO4, K4P |
| 2 | 1095 | 0.81 | 0.82 | 94 | SO4, K4P |
| 3 | 767 | 0.76 | 0.80 | 85 | empty |
| 4 | 69 | 0.49 | 0.84 | 17 | empty |
| 5 | 71 | 0.48 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 448 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6MVO · HCV NS5B 1A Y316 bound to Compound 49 · 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 Q66N85
- Elsewhere: RCSB PDB 6MVO · PDBe 6MVO · UniProt Q66N85
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