MolNFT v1 · #4778 · protein
Inhibition of the hepatitis C virus NS3/4A protease. the crystal structures of two protease-inhibitor complexes (inhibitor I)
1DY9 · PROTEASE/HELICASE NS3 (P70): “Inhibition of the hepatitis C virus NS3/4A protease. the crystal structures of two protease-inhibitor…”. X-ray diffraction, 2 ligands (2ZF, ZN), 1 pocket (best druggability 0.32). MolNFT v1 #4778 on…
- PDB
- 1DY9
- Type
- protein
- Length
- 374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTEASE/HELICASE NS3 (P70); Nonstructural protein NS4A (P4)
- EC
- 3.4.22.-
- UniProt
- Q81755
- Ligands
- 2ZF, ZN
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PROTEASE/HELICASE NS3 (P70) (EC 3.4.22.-) | protein | 175 | 11% helix, 48% strand | Q81755 |
| C, D | Nonstructural protein NS4A (P4) | protein | 12 | 0% helix, 75% strand | Q81755 |
Ligands and binding sites
- 2ZF · N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
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 | 50 | 0.32 | 0.77 | 16 | 2ZF |
Interfaces
3 interfaces between chains.
- B–D · 1224 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1209 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 459 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1DY9 · Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two… · the same entry in another collection · chain C against C, 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 Q81755
- Elsewhere: RCSB PDB 1DY9 · PDBe 1DY9 · UniProt Q81755
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