Research workbench
PDK1 mutant bound to allosteric disulfide fragment activator JS30
Analyse PDK1 mutant bound to allosteric disulfide fragment activator JS30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OTU
- Type
- protein
- Length
- 277 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
- J30, BI4, SO4, CL
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 277 | 41% helix, 19% strand | O15530 |
Ligands and binding sites
- J30 · 4-[4-(naphthalen-1-ylmethyl)piperazin-1-yl]-4-oxobutane-1-thiol · ligand · chains A
- BI4 · 3-(1H-indol-3-yl)-4-{1-[2-(1-methylpyrrolidin-2-yl)ethyl]-1H-indol-3-yl}-1H-pyrrole-2,5-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- CL · Chloride ion · ion · 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 | 306 | 0.59 | 0.78 | 30 | BI4, CL |
| 2 | 85 | 0.32 | 0.73 | 16 | SO4 |
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 3OTU · PDK1 mutant bound to allosteric disulfide fragment activator JS30 · 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 3OTU · PDBe 3OTU · UniProt O15530
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