MolNFT v1 · #106770 · protein
West nile virus non-structural protein 1 (NS1) form 1 crystal
4TPL · West nile virus NS1: “West nile virus non-structural protein 1 (NS1) form 1 crystal”. X-ray diffraction, 5 ligands (OXN, NAG, MAN), 6 pockets (best druggability 0.73). MolNFT v1 #106770 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4TPL
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- West nile virus NS1
- UniProt
- Q5SBG8
- Ligands
- OXN, NAG, MAN, BMA, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | West nile virus NS1 | protein | 342 | 18% helix, 31% strand | Q5SBG8 |
| B | West nile virus NS1 | protein | 352 | 14% helix, 32% strand | Q5SBG8 |
Ligands and binding sites
- OXN · Oxtoxynol-10 · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.73 | 0.98 | 23 | empty |
| 2 | 55 | 0.70 | 0.98 | 21 | empty |
| 3 | 158 | 0.65 | 0.86 | 34 | empty |
| 4 | 166 | 0.44 | 0.75 | 28 | empty |
| 5 | 129 | 0.41 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3195 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4TPL · West Nile Virus Non-structural protein 1 (NS1) Form 1 crystal · 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 Q5SBG8
- Elsewhere: RCSB PDB 4TPL · PDBe 4TPL · UniProt Q5SBG8
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