MolNFT v1 · #134189 · protein
Crystal structure of PI3KALPHA in complex with fragments 6 and 24
5SWP · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Crystal structure of PI3KALPHA in complex with fragments 6 and 24”. X-ray diffraction, 3 ligands (70W, 70V, CL), 17 pockets (best druggability 0.88). MolNFT v1 #134189 on…
- PDB
- 5SWP
- Type
- protein
- Length
- 1,318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform…
- EC
- 2.7.1.153, 2.7.11.1
- UniProt
- P42336, P27986
- Ligands
- 70W, 70V, CL
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153, 2.7.11.1) | protein | 1060 | 40% helix, 15% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 258 | 61% helix, 8% strand | P27986 |
Ligands and binding sites
- 70W · tert-butyl 4-aminopiperidine-1-carboxylate · ligand · 2 copies · chains A
- 70V · 2-methylcyclohexane-1,3-dione · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.88 | 0.90 | 113 | 70V |
| 2 | 352 | 0.82 | 0.91 | 53 | empty |
| 3 | 1189 | 0.81 | 0.83 | 88 | empty |
| 4 | 1136 | 0.81 | 0.82 | 73 | 70W |
| 5 | 189 | 0.66 | 0.85 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 4264 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5SWP · Crystal Structure of PI3Kalpha in complex with fragments 6 and 24 · the same entry in another collection · chain A against A, TM-score 1.00
- P42336 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P42336
- Every structure of UniProt P27986
- Elsewhere: RCSB PDB 5SWP · PDBe 5SWP · UniProt P42336 · UniProt P27986
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