MolNFT v1 · #53822 · protein
The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with 3-methyladenine
2X6F · Phosphotidylinositol 3 kinase 59F: “The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with 3-methyladenine”. X-ray diffraction, 1 ligand (3MA), 13 pockets (best druggability 0.70). MolNFT v1 #53822 on…
- PDB
- 2X6F
- Type
- protein
- Length
- 1,085 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotidylinositol 3 kinase 59F
- EC
- 2.7.1.137, 2.7.1.153, 2.7.1.154
- UniProt
- Q9W1M7
- Ligands
- 3MA
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotidylinositol 3 kinase 59F (EC 2.7.1.137, 2.7.1.153, 2.7.1.154) | protein | 543 | 57% helix, 6% strand | Q9W1M7 |
| B | Phosphotidylinositol 3 kinase 59F (EC 2.7.1.137, 2.7.1.153, 2.7.1.154) | protein | 542 | 57% helix, 8% strand | Q9W1M7 |
Ligands and binding sites
- 3MA · 6-amino-3-methylpurine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.70 | 0.85 | 35 | 3MA |
| 2 | 728 | 0.69 | 0.76 | 79 | empty |
| 3 | 184 | 0.66 | 0.85 | 31 | empty |
| 4 | 268 | 0.65 | 0.82 | 28 | 3MA |
| 5 | 311 | 0.64 | 0.80 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2X6F · The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with… · the same entry in another collection · chain B against B, 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 Q9W1M7
- Elsewhere: RCSB PDB 2X6F · PDBe 2X6F · UniProt Q9W1M7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.