MolNFT v1 · #74505 · protein
HCV NS3/4A in complex with ligand 3
3OYP · Serine protease NS3: “HCV NS3/4A in complex with ligand 3”. X-ray diffraction, 5 ligands (DAL, 0Y8, 0Y9), 3 pockets (best druggability 0.51). MolNFT v1 #74505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OYP
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease NS3; Non-structural protein 4A
- EC
- 3.4.21.98, 3.6.1.15, 3.6.4.13
- UniProt
- P26662
- Ligands
- DAL, 0Y8, 0Y9, 0YA, ZN
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 174 | 12% helix, 47% strand | P26662 |
| B | Serine protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 175 | 12% helix, 48% strand | P26662 |
| C, D | Non-structural protein 4A | protein | 12 | 0% helix, 75% strand | P26662 |
Ligands and binding sites
- DAL · D-alanine · ligand · 2 copies · chains A, B
- 0Y8 · (4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-L-proline · ligand · 2 copies · chains A, B
- 0Y9 · (1R,2S)-1-amino-2-ethenylcyclopropanecarboxylic acid · ligand · 2 copies · chains A, B
- 0YA · Cyclopropanesulfonamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PPI · Propanoic 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 | 99 | 0.51 | 0.82 | 23 | empty |
| 2 | 70 | 0.40 | 0.79 | 18 | 0Y9, 0YA |
| 3 | 63 | 0.38 | 0.79 | 18 | 0Y9, 0YA |
Interfaces
3 interfaces between chains.
- B–D · 1225 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1215 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 249 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (additive adduct, disulfide).
Compared structures
- 3OYP · HCV NS3/4A in complex with ligand 3 · 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 P26662
- Elsewhere: RCSB PDB 3OYP · PDBe 3OYP · UniProt P26662
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