MolNFT v2 · #194365 · protein
Nipah virus matrix protein in complex with PI(4,5)P2
7SKU: “Nipah virus matrix protein in complex with PI(4,5)P2”. X-ray diffraction at 2.117, 2 ligands (PIO, SO4), 9 pockets (best druggability 0.78). MolNFT v2 #194365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SKU
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.117
- Source
- Nipah virus
- Molecule
- Matrix protein
- UniProt
- Q9IK90
- Ligands
- PIO, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.117 · 2 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix protein | protein | 301 | 18% helix, 43% strand | Q9IK90 |
| B | Matrix protein | protein | 299 | 20% helix, 42% strand | Q9IK90 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.78 | 0.80 | 107 | PIO |
| 2 | 98 | 0.69 | 0.92 | 33 | empty |
| 3 | 93 | 0.68 | 0.92 | 30 | empty |
| 4 | 287 | 0.68 | 0.83 | 31 | PIO |
| 5 | 114 | 0.48 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3505 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7SKU · Nipah virus matrix protein in complex with PI(4,5)P2 · 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 Q9IK90
- Elsewhere: RCSB PDB 7SKU · PDBe 7SKU · UniProt Q9IK90
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