Research workbench
Crystal structure of HCV NS5B polymerase in complex with [(1R)-5,8- dichloro-1-propyl-1,3,4,9-TETRAHYDROPYRANO[3,4-B]INDOL-1-YL]ACETIC acid
Analyse Crystal structure of HCV NS5B polymerase in complex with [(1R)-5,8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J02
- 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
- 1JE, NA, SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% 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 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- 1JE · [(1R)-5,8-dichloro-1-propyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.80 | 0.81 | 89 | SO4 |
| 2 | 1150 | 0.80 | 0.81 | 91 | SO4, NA |
| 3 | 98 | 0.52 | 0.83 | 20 | empty |
| 4 | 120 | 0.46 | 0.79 | 24 | empty |
| 5 | 127 | 0.46 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4J02 · 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 4J02 · PDBe 4J02 · UniProt O92972
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