MolNFT v1 · #95760 · protein
Crystal structure of HCV NS5B polymerase in complex with 4-chloro-2- {[(2,4,5-TRICHLOROPHENYL)SULFONYL]AMINO}BENZOIC acid
4J04 · Genome polyprotein: “Crystal structure of HCV NS5B polymerase in complex with 4-chloro-2…”. X-ray diffraction, 2 ligands (1JF, MN), 14 pockets (best druggability 0.81). MolNFT v1 #95760 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4J04
- Type
- protein
- Length
- 1,117 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
- UniProt
- O92972
- Ligands
- 1JF, MN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 559 | 49% helix, 15% strand | O92972 |
| B | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 558 | 47% helix, 15% strand | O92972 |
Ligands and binding sites
- 1JF · 4-chloro-2-{[(2,4,5-trichlorophenyl)sulfonyl]amino}benzoic acid · ligand · 3 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.81 | 0.82 | 93 | MN |
| 2 | 1160 | 0.80 | 0.82 | 83 | MN |
| 3 | 129 | 0.52 | 0.81 | 19 | empty |
| 4 | 137 | 0.49 | 0.79 | 19 | empty |
| 5 | 116 | 0.46 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1005 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4J04 · Crystal structure of hcv ns5b polymerase in complex with… · 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 4J04 · PDBe 4J04 · UniProt O92972
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