MolNFT v1 · #181673 · protein
Structure of zika virus NS2B-NS3 protease mutant binding the compound NSC86314 in the super-open conformation
7M1V · Core protein: “Structure of zika virus NS2B-NS3 protease mutant binding the compound NSC86314 in the super-open conformation”. X-ray diffraction, 2 ligands (YO1, CL), 2 pockets (best druggability 0.78). MolNFT v1 #181673 on…
- PDB
- 7M1V
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- A0A219YLK5
- Ligands
- YO1, CL
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 166 | 4% helix, 48% strand | A0A219YLK5 |
| B | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 163 | 2% helix, 46% strand | A0A219YLK5 |
Ligands and binding sites
- YO1 · 4-(2-{2,4-diamino-5-[2-(4-{[(2E)-1,3-thiazolidin-2-ylidene]sulfamoyl}phenyl) hydrazinyl]phenyl}hydrazinyl)-N-[(2S)-1,3-thiazolidin-2-yl]benzene-1-sulfonamide · ligand · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.78 | 0.81 | 86 | CL, EDO |
| 2 | 137 | 0.48 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 975 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7M1V · Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the… · 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 A0A219YLK5
- Elsewhere: RCSB PDB 7M1V · PDBe 7M1V · UniProt A0A219YLK5
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