Research workbench
Crystal structure of PI3KALPHA in complex with fragment 14
Analyse Crystal structure of PI3KALPHA in complex with fragment 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SX9
- Type
- protein
- Length
- 1,284 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
- 71L
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% 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 | 1045 | 41% helix, 16% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 239 | 66% helix, 2% strand | P27986 |
Ligands and binding sites
- 71L · 4,6-dimethylpyridin-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.87 | 0.88 | 115 | 71L |
| 2 | 1024 | 0.84 | 0.84 | 89 | empty |
| 3 | 914 | 0.83 | 0.85 | 67 | empty |
| 4 | 600 | 0.80 | 0.85 | 49 | empty |
| 5 | 251 | 0.64 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 3773 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5SX9 · Crystal Structure of PI3Kalpha in complex with fragment 14 · 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 5SX9 · PDBe 5SX9 · UniProt P42336 · UniProt P27986
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