Research workbench
X-ray crystal structure of hepatitis C virus RNA-dependent RNA polymerase in complex with non-nucleoside analogue inhibitor
Analyse X-ray crystal structure of hepatitis C virus RNA-dependent RNA polymerase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D3Z
- Type
- protein
- Length
- 1,119 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- EC
- 2.7.7.48
- UniProt
- Q99AU2
- Ligands
- FIH
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein (EC 2.7.7.48) | protein | 560 | 49% helix, 15% strand | Q99AU2 |
| B | Polyprotein (EC 2.7.7.48) | protein | 559 | 48% helix, 14% strand | Q99AU2 |
Ligands and binding sites
- FIH · 5-(4-fluorophenyl)-3-{[(4-methylphenyl) sulfonyl]amino}thiophene-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.80 | 0.81 | 85 | empty |
| 2 | 1038 | 0.79 | 0.81 | 80 | empty |
| 3 | 993 | 0.74 | 0.77 | 63 | empty |
| 4 | 133 | 0.52 | 0.80 | 20 | empty |
| 5 | 126 | 0.50 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2D3Z · X-ray crystal structure of hepatitis C virus RNA-dependent RNA polymerase in complex with… · 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 Q99AU2
- Elsewhere: RCSB PDB 2D3Z · PDBe 2D3Z · UniProt Q99AU2
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