Research workbench
Crystal structure of HCV NS3/NS4A protease complexed with ddivpc peptide
Analyse Crystal structure of HCV NS3/NS4A protease complexed with ddivpc peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JMY
- Type
- protein
- Length
- 402 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; HCV non-structural protein 4A; Substrate peptide
- EC
- 3.4.21.98
- UniProt
- Q81817
- Ligands
- ZN, NA
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyprotein (EC 3.4.21.98) | protein | 182 | 15% helix, 43% strand | Q81817 |
| C, D | HCV non-structural protein 4A | protein | 13 | 0% helix, 69% strand | — |
| E, F | Substrate peptide | protein | 6 | 0% helix, 67% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.39 | 0.78 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1217 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1199 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 467 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 444 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 428 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4JMY · Crystal structure of HCV NS3/NS4A protease complexed with DDIVPC peptide · 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 Q81817
- Elsewhere: RCSB PDB 4JMY · PDBe 4JMY · UniProt Q81817
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