MolNFT v1 · #25642 · protein
Crystal structure of the PDK1 pleckstrin homology (pH) domain
1W1H · 3-phosphoinositide dependent protein kinase-1: “Crystal structure of the PDK1 pleckstrin homology (pH) domain”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.48). MolNFT v1 #25642 on GenesisL1: 3D structure…
- PDB
- 1W1H
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- 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
- SO4
- Pockets
- 11 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide dependent protein kinase-1 (EC 2.7.1.37) | protein | 147 | 25% helix, 37% strand | O15530 |
| B | 3-phosphoinositide dependent protein kinase-1 (EC 2.7.1.37) | protein | 151 | 26% helix, 38% strand | O15530 |
| C | 3-phosphoinositide dependent protein kinase-1 (EC 2.7.1.37) | protein | 138 | 26% helix, 41% strand | O15530 |
| D | 3-phosphoinositide dependent protein kinase-1 (EC 2.7.1.37) | protein | 137 | 28% helix, 42% strand | O15530 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 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 | 0.48 | 0.83 | 17 | empty |
| 2 | 97 | 0.46 | 0.80 | 18 | empty |
| 3 | 67 | 0.46 | 0.83 | 16 | empty |
| 4 | 93 | 0.45 | 0.80 | 19 | GOL |
| 5 | 80 | 0.40 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–D · 436 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 293 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1W1H · Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.94
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 1W1H · PDBe 1W1H · UniProt O15530
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