Research workbench
Crystal structure of PDK1 in complex with ATP and piftide
Analyse Crystal structure of PDK1 in complex with ATP and piftide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RRV
- Type
- protein
- Length
- 293 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1; SERINE/THREONINE-protein kinase N2
- EC
- 2.7.11.1
- UniProt
- O15530, Q16513
- Ligands
- ATP
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 284 | 40% helix, 18% strand | O15530 |
| B | SERINE/THREONINE-protein kinase N2 | protein | 9 | 0% helix, 22% strand | Q16513 |
Ligands and binding sites
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 | 363 | 0.63 | 0.78 | 37 | ATP |
| 2 | 77 | 0.38 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 588 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4RRV · Crystal structure of PDK1 in complex with ATP and PIFtide · the same entry in another collection · chain A against A, TM-score 1.00
- Q16513 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase N2 (Q16513) · a predicted model of the same protein · chain B against A, TM-score 0.66
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
- Every structure of UniProt Q16513
- Elsewhere: RCSB PDB 4RRV · PDBe 4RRV · UniProt O15530 · UniProt Q16513
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