Research workbench
Hepatitis C virus polymerase NS5B genotype 1B (bk) in complex with RG7109 (N-{4-[6-tert-butyl-5-methoxy-8-(6-methoxy-2-oxo-2,5- dihydropyridin-3-YL)QUINOLIN-3-YL]PHENYL}METHANESULFONAMIDE)
Analyse Hepatitis C virus polymerase NS5B genotype 1B (bk) in complex with RG7109… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MIA
- Type
- protein
- Length
- 1,091 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
- P26663
- Ligands
- 28L, ZN
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 546 | 47% helix, 15% strand | P26663 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 545 | 49% helix, 16% strand | P26663 |
Ligands and binding sites
- 28L · N-{4-[6-tert-butyl-5-methoxy-8-(6-methoxy-2-oxo-2,5-dihydropyridin-3-yl)quinolin-3-yl]phenyl}methanesulfonamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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 | 1117 | 0.81 | 0.82 | 84 | 28L |
| 2 | 1144 | 0.80 | 0.82 | 81 | 28L |
| 3 | 565 | 0.73 | 0.81 | 69 | empty |
| 4 | 203 | 0.63 | 0.83 | 27 | empty |
| 5 | 75 | 0.48 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 684 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4MIA · Hepatitis C Virus polymerase NS5B genotype 1b (BK) in complex with RG7109… · 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 4MIA · PDBe 4MIA · UniProt P26663
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