MolNFT v1 · #131943 · protein
Crystal structure of the hepatitis C virus genotype 2A strain JFH1 L30S NS5B RNA-dependent RNA polymerase in complex with 6- (ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl) CYCLOPROPYL]CARBAMOYL}-4-methoxyphenyl)-N-methyl-1-benzofuran-3- carboxamide
5QJ1: “Crystal structure of the hepatitis C virus genotype 2A strain JFH1 L30S NS5B RNA-dependent RNA polymerase in…”. X-ray diffraction, 2 ligands (J6J, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #131943 on GenesisL1: 3D…
- PDB
- 5QJ1
- Type
- protein
- Length
- 543 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- EC
- 2.7.7.48
- UniProt
- R9THT8
- Ligands
- J6J, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 543 | 50% helix, 16% strand | R9THT8 |
Ligands and binding sites
- J6J · 6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 11 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · 3 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 | 820 | 0.80 | 0.82 | 80 | J6J, GOL, PG4 |
| 2 | 176 | 0.53 | 0.79 | 28 | SO4 |
| 3 | 145 | 0.45 | 0.77 | 28 | PG4 |
| 4 | 107 | 0.43 | 0.78 | 19 | empty |
| 5 | 121 | 0.43 | 0.76 | 22 | SO4 |
Compared structures
- 5QJ1 · CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B… · 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 R9THT8
- Elsewhere: RCSB PDB 5QJ1 · PDBe 5QJ1 · UniProt R9THT8
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