Research workbench
Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with 4-fluoro-2-(4-fluorophenyl)-N-methyl-5-(2- methyl-5-{[1-(pyrimidin-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1- benzofuran-3-carboxamide (bms-929075)
Analyse Crystal structure of the hepatitis C virus NS5B 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
- 5PZP
- Type
- protein
- Length
- 1,080 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
- Q9WMX2
- Ligands
- 23E, 8XJ, SO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 545 | 48% helix, 17% strand | Q9WMX2 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 535 | 49% helix, 16% strand | Q9WMX2 |
Ligands and binding sites
- 23E · (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
- 8XJ · 4-fluoro-2-(4-fluorophenyl)-N-methyl-5-(2-methyl-5-{[1-(pyrimidin-2-yl)cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.83 | 0.84 | 94 | 8XJ |
| 2 | 1194 | 0.83 | 0.84 | 110 | 8XJ |
| 3 | 110 | 0.50 | 0.81 | 17 | empty |
| 4 | 110 | 0.45 | 0.78 | 21 | empty |
| 5 | 108 | 0.44 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 955 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5PZP · Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex… · 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 Q9WMX2
- Elsewhere: RCSB PDB 5PZP · PDBe 5PZP · UniProt Q9WMX2
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