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Crystal structure of zika virus NS3 protease in complex with a dipeptide inhibitor
Analyse Crystal structure of zika virus NS3 protease in complex with a dipeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YOF
- Type
- protein
- Length
- 195 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS2B cofactor; NS3 protease
- Ligands
- 7HS
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS2B cofactor | protein | 39 | 0% helix, 46% strand | — |
| B | NS3 protease | protein | 156 | 4% helix, 46% strand | — |
Ligands and binding sites
- 7HS · (S)-2-acetamido-6-amino-N-((S)-5-guanidino-1-oxopentan-2-yl)hexanamide · ligand · chains A, 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 | 116 | 0.38 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2017 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5YOF · Crystal structure of zika virus NS3 protease in complex with a dipeptide 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
- Elsewhere: RCSB PDB 5YOF · PDBe 5YOF
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