MolNFT v1 · #25639 · protein
Crystal structure of the PDK1 pleckstrin homology (pH) domain bound to inositol (1,3,4,5)-tetrakisphosphate
1W1D · 3-phosphoinositide dependent protein kinase-1: “Crystal structure of the PDK1 pleckstrin homology (pH) domain bound to inositol (1,3,4,5)-tetrakisphosphate”. X-ray diffraction, 2 ligands (4IP, AU), 2 pockets (best druggability…
- PDB
- 1W1D
- Type
- protein
- Length
- 143 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
- 4IP, AU
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide dependent protein kinase-1 (EC 2.7.1.37) | protein | 143 | 26% helix, 42% strand | O15530 |
Ligands and binding sites
- 4IP · Inositol-(1,3,4,5)-tetrakisphosphate · ligand · chains A
- AU · Gold ion · metal · chains A
- GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.43 | 0.81 | 17 | empty |
| 2 | 78 | 0.37 | 0.76 | 12 | empty |
Compared structures
- 1W1D · Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol… · 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 0.92
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 1W1D · PDBe 1W1D · UniProt O15530
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