Research workbench
Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor pha-00729145
Analyse Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YVF
- Type
- protein
- Length
- 564 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV NS5B polymerase
- EC
- 2.7.7.48
- UniProt
- O93077
- Ligands
- PH7, PO4, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCV NS5B polymerase (EC 2.7.7.48) | protein | 564 | 46% helix, 16% strand | O93077 |
Ligands and binding sites
- PH7 · (2Z)-2-(benzoylamino)-3-[4-(2-bromophenoxy)phenyl]-2-propenoic acid · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.79 | 0.81 | 80 | PH7, GOL |
| 2 | 150 | 0.48 | 0.77 | 19 | empty |
| 3 | 117 | 0.44 | 0.77 | 27 | empty |
| 4 | 67 | 0.42 | 0.81 | 18 | empty |
| 5 | 86 | 0.38 | 0.77 | 14 | empty |
Compared structures
- 1YVF · Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145 · 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 O93077
- Elsewhere: RCSB PDB 1YVF · PDBe 1YVF · UniProt O93077
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