MolNFT v1 · #20502 · protein
M9A HCV protease complex with pentapeptide keto-amide inhibitor
1RGQ · NS3 protease: “M9A HCV protease complex with pentapeptide keto-amide inhibitor”. X-ray diffraction, 2 ligands (AKP, ZN), 5 pockets (best druggability 0.60). MolNFT v1 #20502 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1RGQ
- Type
- protein
- Length
- 379 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 protease; NS4A peptide
- EC
- 3.4.21.98
- UniProt
- P27958, O39914
- Ligands
- AKP, ZN
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3 protease (EC 3.4.21.98) | protein | 154 | 11% helix, 49% strand | P27958 |
| B | NS3 protease (EC 3.4.21.98) | protein | 186 | 15% helix, 44% strand | P27958 |
| C | NS4A peptide | protein | 22 | 0% helix, 45% strand | O39914 |
| D | NS4A peptide | protein | 17 | 0% helix, 53% strand | O39914 |
Ligands and binding sites
- AKP · N-(pyrazin-2-ylcarbonyl)leucylisoleucyl-N~1~-{1-[2-({1-carboxy-2-[4-(phosphonooxy)phenyl]ethyl}amino)-1,1-dihydroxy-2-oxoethyl]but-3-enyl}-3-cyclohexylalaninamide · ligand · chains B
- 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.60 | 0.83 | 27 | empty |
| 2 | 51 | 0.41 | 0.82 | 21 | empty |
| 3 | 74 | 0.34 | 0.76 | 18 | empty |
| 4 | 62 | 0.33 | 0.76 | 17 | empty |
| 5 | 53 | 0.26 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1342 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 921 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 477 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 340 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 239 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1RGQ · M9A HCV Protease complex with pentapeptide keto-amide inhibitor · 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 P27958
- Every structure of UniProt O39914
- Elsewhere: RCSB PDB 1RGQ · PDBe 1RGQ · UniProt P27958 · UniProt O39914
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