MolNFT v1 · #21594 · protein
Core (C) protein from west nile virus, subtype kunjin
1SFK · Core protein: “Core (C) protein from west nile virus, subtype kunjin”. X-ray diffraction, 3 ligands (CA, CL, PO4), 10 pockets (best druggability 0.71). MolNFT v1 #21594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SFK
- Type
- protein
- Length
- 553 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein
- UniProt
- P14335
- Ligands
- CA, CL, PO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G | Core protein | protein | 73 | 75% helix, 0% strand | P14335 |
| B | Core protein | protein | 57 | 74% helix, 0% strand | P14335 |
| H | Core protein | protein | 58 | 72% helix, 0% strand | P14335 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, F, G
- CL · Chloride ion · ion · 4 copies · chains A, D, F, G
- PO4 · Phosphate ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.71 | 0.88 | 20 | PG4 |
| 2 | 134 | 0.71 | 0.89 | 18 | PG4 |
| 3 | 534 | 0.65 | 0.76 | 44 | empty |
| 4 | 206 | 0.62 | 0.83 | 30 | empty |
| 5 | 119 | 0.61 | 0.86 | 19 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1778 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1736 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1551 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 1540 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 509 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1SFK · Core (C) protein from West Nile Virus, subtype Kunjin · 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 P14335
- Elsewhere: RCSB PDB 1SFK · PDBe 1SFK · UniProt P14335
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