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Crystal structure of human phosphoinositide-dependent protein kinase 1 (PDK1) 5-hydroxy-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-1,3-dihydro- indol-2-one complex
Analyse Crystal structure of human phosphoinositide-dependent protein kinase 1 (PDK1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PE0
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1
- EC
- 2.7.11.1
- UniProt
- O15530
- Ligands
- 39Z, SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 276 | 41% helix, 18% strand | O15530 |
Ligands and binding sites
- 39Z · 5-hydroxy-3-[(1R)-1-(1H-pyrrol-2-yl)ethyl]-2H-indol-2-one · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.68 | 0.81 | 35 | 39Z, GOL |
| 2 | 88 | 0.31 | 0.72 | 19 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2PE0 · CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1)… · the same entry in another collection · chain A against A, TM-score 1.00
- O15530 · AlphaFold monomer V2.0 prediction for 3-phosphoinositide-dependent protein kinase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O15530
- Elsewhere: RCSB PDB 2PE0 · PDBe 2PE0 · UniProt O15530
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