MolNFT v1 · #179349 · protein
PIKFYVE/FIG4/VAC14 complex centered on pikfyve - MAP2
7K2V · 1-phosphatidylinositol 3-phosphate 5-kinase: “PIKFYVE/FIG4/VAC14 complex centered on pikfyve - MAP2”. Electron microscopy, 11 pockets (best druggability 0.85). MolNFT v1 #179349 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7K2V
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-phosphatidylinositol 3-phosphate 5-kinase
- EC
- 2.7.1.150
- UniProt
- Q9Y2I7, E9PDH4
- Pockets
- 11 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 1-phosphatidylinositol 3-phosphate 5-kinase (EC 2.7.1.150) | protein | 264 | 32% helix, 19% strand | Q9Y2I7 |
| A | 1-phosphatidylinositol 3-phosphate 5-kinase | protein | 450 | 37% helix, 10% strand | E9PDH4 |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.85 | 0.87 | 92 | empty |
| 2 | 174 | 0.79 | 0.94 | 31 | empty |
| 3 | 790 | 0.77 | 0.80 | 79 | empty |
| 4 | 392 | 0.72 | 0.83 | 58 | empty |
| 5 | 421 | 0.68 | 0.80 | 48 | empty |
Interfaces
1 interface between chains.
- P–A · 156 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7K2V · PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2 · the same entry in another collection · chain P against P, TM-score 1.00
- Q9Y2I7 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol 3-phosphate 5-kinase (Q9Y2I7) · a predicted model of the same protein · chain P against A, TM-score 0.83
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 Q9Y2I7
- Every structure of UniProt E9PDH4
- Elsewhere: RCSB PDB 7K2V · PDBe 7K2V · UniProt Q9Y2I7 · UniProt E9PDH4
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