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The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with pi-103
Analyse The crystal structure of the drosophila class III PI3-kinase VPS34 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X6K
- Type
- protein
- Length
- 1,100 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
- X6K, SO4
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% 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 | 550 | 56% helix, 7% strand | Q9W1M7 |
| B | Phosphotidylinositol 3 kinase 59F (EC 2.7.1.137, 2.7.1.153, 2.7.1.154) | protein | 550 | 59% helix, 8% strand | Q9W1M7 |
Ligands and binding sites
- X6K · 3-(4-morpholin-4-ylpyrido[3',2':4,5]furo[3,2-d]pyrimidin-2-yl)phenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.69 | 0.83 | 25 | SO4, X6K |
| 2 | 712 | 0.68 | 0.76 | 74 | empty |
| 3 | 320 | 0.66 | 0.81 | 36 | X6K |
| 4 | 226 | 0.66 | 0.83 | 31 | empty |
| 5 | 177 | 0.65 | 0.85 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1634 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2X6K · The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with pi-103 · 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 Q9W1M7
- Elsewhere: RCSB PDB 2X6K · PDBe 2X6K · UniProt Q9W1M7
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