Research workbench
Zika virus non-structural protein 1 (NS1)
Analyse Zika virus non-structural protein 1 (NS1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K6K
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zika virus protein
- UniProt
- Q32ZE1
- Ligands
- NAG, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zika virus protein | protein | 350 | 15% helix, 31% strand | Q32ZE1 |
| B | Zika virus protein | protein | 354 | 16% helix, 31% strand | Q32ZE1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.75 | 0.98 | 21 | empty |
| 2 | 80 | 0.75 | 0.97 | 23 | empty |
| 3 | 82 | 0.72 | 0.96 | 27 | empty |
| 4 | 174 | 0.49 | 0.77 | 27 | empty |
| 5 | 81 | 0.49 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2823 Ų buried · 73 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5K6K · Zika virus non-structural protein 1 (NS1) · 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 Q32ZE1
- Elsewhere: RCSB PDB 5K6K · PDBe 5K6K · UniProt Q32ZE1
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