Research workbench
Crystal structure of the PI3KC2ALPHA C2 domain in complex with IP6
Analyse Crystal structure of the PI3KC2ALPHA C2 domain in complex with IP6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BU0
- Type
- protein
- Length
- 377 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-phosphate 3-kinase C2 domain- containing subunit alpha
- EC
- 2.7.1.154
- UniProt
- O00443
- Ligands
- IHP, O4B
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4-phosphate 3-kinase C2 domain- containing subunit alpha (EC 2.7.1.154) | protein | 123 | 6% helix, 50% strand | O00443 |
| B | Phosphatidylinositol 4-phosphate 3-kinase C2 domain- containing subunit alpha (EC 2.7.1.154) | protein | 126 | 6% helix, 52% strand | O00443 |
| C | Phosphatidylinositol 4-phosphate 3-kinase C2 domain- containing subunit alpha (EC 2.7.1.154) | protein | 128 | 5% helix, 52% strand | O00443 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · chains A, C
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.58 | 0.75 | 42 | FMT, IHP |
Interfaces
2 interfaces between chains.
- A–C · 499 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 427 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6BU0 · Crystal structure of the PI3KC2alpha C2 domain in complex with IP6 · the same entry in another collection · chain A against A, TM-score 1.00
- O00443 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-phosphate 3-kinase C2… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O00443
- Elsewhere: RCSB PDB 6BU0 · PDBe 6BU0 · UniProt O00443
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