MolNFT v1 · #101924 · protein
West nile virus non-structural protein 1 (NS1) form 2 crystal
4O6C: “West nile virus non-structural protein 1 (NS1) form 2 crystal”. X-ray diffraction, 2 ligands (NAG, SO4), 20 pockets (best druggability 0.76). MolNFT v1 #101924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4O6C
- Type
- protein
- Length
- 2,028 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS1
- UniProt
- U3N977
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | NS1 | protein | 338 | 14% helix, 33% strand | U3N977 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.76 | 0.79 | 101 | SO4 |
| 2 | 61 | 0.72 | 0.98 | 22 | empty |
| 3 | 65 | 0.72 | 0.98 | 22 | empty |
| 4 | 160 | 0.70 | 0.89 | 35 | empty |
| 5 | 57 | 0.69 | 0.97 | 20 | empty |
Interfaces
8 interfaces between chains.
- E–F · 2450 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2447 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2445 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4O6C · West Nile Virus Non-structural protein 1 (NS1) Form 2 crystal · the same entry in another collection · chain E against E, 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 U3N977
- Elsewhere: RCSB PDB 4O6C · PDBe 4O6C · UniProt U3N977
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