MolNFT v1 · #29027 · protein
Hepatitis C virus RNA polymerase genotype 2A in complex with non- nucleoside analogue inhibitor
1YVZ · RNA dependent RNA polymerase: “Hepatitis C virus RNA polymerase genotype 2A in complex with non- nucleoside analogue inhibitor”. X-ray diffraction, 2 ligands (JPC, SO4), 7 pockets (best druggability 0.74). MolNFT v1 #29027 on…
- PDB
- 1YVZ
- Type
- protein
- Length
- 548 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase
- UniProt
- P26660
- Ligands
- JPC, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase | protein | 548 | 48% helix, 16% strand | P26660 |
Ligands and binding sites
- JPC · 3-[(2,4-dichlorobenzoyl)(isopropyl)amino]-5-phenylthiophene-2-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 7 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.74 | 0.81 | 69 | empty |
| 2 | 234 | 0.58 | 0.79 | 31 | SO4 |
| 3 | 132 | 0.42 | 0.75 | 25 | empty |
| 4 | 53 | 0.40 | 0.81 | 16 | empty |
| 5 | 61 | 0.39 | 0.80 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1YVZ · Hepatitis C Virus RNA Polymerase Genotype 2a In Complex With Non- Nucleoside Analogue… · 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 P26660
- Elsewhere: RCSB PDB 1YVZ · PDBe 1YVZ · UniProt P26660
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