MolNFT v1 · #157600 · protein
Crystal structure of the designed protein DNCR2/DANOPREVIR/NS3A complex
6N4N · NS3 protease: “Crystal structure of the designed protein DNCR2/DANOPREVIR/NS3A complex”. X-ray diffraction, 3 ligands (TSV, ZN, SO4), 10 pockets (best druggability 0.89). MolNFT v1 #157600 on GenesisL1: 3D structure, binding sites…
- PDB
- 6N4N
- Type
- protein
- Length
- 765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 protease; Rosetta-designed DANOPREVIR/NS3A complex reader 2
- EC
- 3.4.21.-
- UniProt
- A0A0B4WYC6
- Ligands
- TSV, ZN, SO4
- Pockets
- 10 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NS3 protease (EC 3.4.21.-) | protein | 195 | 12% helix, 44% strand | A0A0B4WYC6 |
| C | Rosetta-designed DANOPREVIR/NS3A complex reader 2 | protein | 184 | 86% helix, 0% strand | — |
| F | Rosetta-designed DANOPREVIR/NS3A complex reader 2 | protein | 191 | 84% helix, 0% strand | — |
Ligands and binding sites
- TSV · (2R,6S,12Z,13aS,14aR,16aS)-6-[(tert-butoxycarbonyl)amino]-14a-[(cyclopropylsulfonyl)carbamoyl]-5,16-dioxo-1,2,3,5,6,7,8 ,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-2-yl 4-fluoro-2H-isoindole-2-carboxylate · ligand · 2 copies · chains A, F, B, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.89 | 0.90 | 129 | TSV |
| 2 | 244 | 0.67 | 0.84 | 30 | empty |
| 3 | 455 | 0.65 | 0.78 | 71 | empty |
| 4 | 122 | 0.53 | 0.82 | 26 | empty |
| 5 | 179 | 0.45 | 0.75 | 34 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 724 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 702 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 673 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 254 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 252 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6N4N · Crystal structure of the designed protein DNCR2/danoprevir/NS3a complex · 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 A0A0B4WYC6
- Elsewhere: RCSB PDB 6N4N · PDBe 6N4N · UniProt A0A0B4WYC6
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