Research workbench
HCV NS3/4A protease domain of genotype 1A3A chimera in complex with grazoprevir
Analyse HCV NS3/4A protease domain of genotype 1A3A chimera in complex with grazoprevir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P6Q
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 4A,SERINE protease NS3
- EC
- 3.4.21.98, 3.6.1.15, 3.6.4.13
- UniProt
- P26664
- Ligands
- SUE, ZN, SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 4A,SERINE protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 197 | 12% helix, 44% strand | P26664 |
| B | Non-structural protein 4A,SERINE protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 196 | 13% helix, 45% strand | P26664 |
Ligands and binding sites
- SUE · (1aR,5S,8S,10R,22aR)-5-tert-butyl-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-14-methoxy-3,6-di oxo-1,1a,3,4,5,6,9,10,18,19,20,21,22,22a-tetradecahydro-8H-7,10-methanocyclopropa[18,19][1,10,3,6]dioxadiazacyclononadec ino[11,12-b]quinoxaline-8-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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 | 346 | 0.58 | 0.76 | 39 | SO4, SUE |
| 2 | 79 | 0.31 | 0.73 | 20 | empty |
| 3 | 59 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 145 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6P6Q · HCV NS3/4A protease domain of genotype 1a3a chimera in complex with grazoprevir · 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 P26664
- Elsewhere: RCSB PDB 6P6Q · PDBe 6P6Q · UniProt P26664
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