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Crystal structure of human PDK1 kinase domain in complex with an allosteric activator bound to the pif-pocket
Analyse Crystal structure of human PDK1 kinase domain in complex with an allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HRF
- Type
- protein
- Length
- 285 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1
- UniProt
- O15530
- Ligands
- ATP, P47
- Pockets
- 2 · best druggability 0.67
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 | protein | 285 | 41% helix, 18% strand | O15530 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- P47 · (2Z)-5-(4-chlorophenyl)-3-phenylpent-2-enoic acid · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 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 | 389 | 0.67 | 0.80 | 35 | ATP |
| 2 | 60 | 0.34 | 0.77 | 12 | P47 |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3HRF · Crystal structure of Human PDK1 kinase domain in complex with an allosteric activator… · 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 O15530
- Elsewhere: RCSB PDB 3HRF · PDBe 3HRF · UniProt O15530
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