Research workbench
Structure of human PDK1 kinase domain in complex with bim-2
Analyse Structure of human PDK1 kinase domain in complex with bim-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UU7
- Type
- protein
- Length
- 281 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide dependent protein kinase-1
- EC
- 2.7.1.37
- UniProt
- O15530
- Ligands
- BI2, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide dependent protein kinase-1 (EC 2.7.1.37) | protein | 281 | 41% helix, 17% strand | O15530 |
Ligands and binding sites
- BI2 · 3-(1H-indol-3-yl)-4-(1-{2-[(2S)-1-methylpyrrolidinyl]ethyl}-1H-indol-3-yl)-1H-pyrrole-2,5-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.64 | 0.78 | 34 | BI2, SO4 |
| 2 | 71 | 0.30 | 0.74 | 23 | GOL, SO4 |
| 3 | 59 | 0.30 | 0.75 | 15 | SO4 |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1UU7 · Structure of human PDK1 kinase domain in complex with BIM-2 · 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 0.98
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 1UU7 · PDBe 1UU7 · UniProt O15530
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