Research workbench
HCV NS5B polymerase complexed with pyridonylindole compound
Analyse HCV NS5B polymerase complexed with pyridonylindole compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YOJ
- Type
- protein
- Length
- 1,121 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
- O92972
- Ligands
- 8Y6, PO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 563 | 49% helix, 15% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 558 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- 8Y6 · 4-fluoranyl-6-[(7-fluoranyl-4-oxidanylidene-3H-quinazolin-6-yl)methyl]-8-(2-oxidanylidene-1H-pyridin-3-yl)furo[2,3-e]indole-7-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.81 | 0.82 | 83 | 8Y6, PO4 |
| 2 | 1123 | 0.80 | 0.81 | 80 | 8Y6, PO4 |
| 3 | 94 | 0.47 | 0.81 | 16 | empty |
| 4 | 103 | 0.47 | 0.80 | 18 | empty |
| 5 | 108 | 0.44 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 993 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2YOJ · HCV NS5B polymerase complexed with pyridonylindole compound · 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 O92972
- Elsewhere: RCSB PDB 2YOJ · PDBe 2YOJ · UniProt O92972
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