MolNFT v1 · #31494 · protein
Hepatitis C virus NS5B RNA polymerase in complex with a covalent inhibitor (5X)
2AX0 · Genome polyprotein: “Hepatitis C virus NS5B RNA polymerase in complex with a covalent inhibitor (5X)”. X-ray diffraction, 2 ligands (5X, SO4), 16 pockets (best druggability 0.79). MolNFT v1 #31494 on GenesisL1: 3D structure, binding…
- PDB
- 2AX0
- Type
- protein
- Length
- 1,111 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 2.7.7.48
- UniProt
- P26663
- Ligands
- 5X, SO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 2.7.7.48) | protein | 554 | 49% helix, 15% strand | P26663 |
| B | Genome polyprotein (EC 2.7.7.48) | protein | 557 | 48% helix, 15% strand | P26663 |
Ligands and binding sites
- 5X · 5R-(2E-methyl-3-phenyl-allyl)-3-(benzenesulfonylamino)-4-oxo-2-thionothiazolidine · 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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.79 | 0.81 | 77 | SO4, 5X |
| 2 | 605 | 0.78 | 0.83 | 70 | SO4, 5X |
| 3 | 334 | 0.54 | 0.74 | 34 | empty |
| 4 | 119 | 0.50 | 0.80 | 17 | empty |
| 5 | 119 | 0.48 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2AX0 · Hepatitis C Virus NS5b RNA Polymerase in complex with a covalent inhibitor (5x) · 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 P26663
- Elsewhere: RCSB PDB 2AX0 · PDBe 2AX0 · UniProt P26663
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