Research workbench
The HCV NS3/NS4A protease apo structure
Analyse The HCV NS3/NS4A protease apo structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KF2
- Type
- protein
- Length
- 372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; 19-mer peptide from genome polyprotein
- EC
- 3.4.21.98
- UniProt
- B1PBR5, Q6GYR8
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein (EC 3.4.21.98) | protein | 154 | 10% helix, 48% strand | B1PBR5 |
| C | 19-mer peptide from genome polyprotein | protein | 16 | 0% helix, 50% strand | Q6GYR8 |
| B | Polyprotein (EC 3.4.21.98) | protein | 181 | 14% helix, 43% strand | B1PBR5 |
| D | 19-mer peptide from genome polyprotein | protein | 21 | 0% helix, 48% strand | Q6GYR8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.56 | 0.84 | 25 | empty |
| 2 | 101 | 0.41 | 0.77 | 22 | empty |
| 3 | 53 | 0.29 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1293 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 855 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 326 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KF2 · The HCV NS3/NS4A protease apo structure · 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 B1PBR5
- Every structure of UniProt Q6GYR8
- Elsewhere: RCSB PDB 3KF2 · PDBe 3KF2 · UniProt B1PBR5 · UniProt Q6GYR8
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