Research workbench
Crystal structure of PDK1 in complex with ATP and the pif-pocket ligand RF4
Analyse Crystal structure of PDK1 in complex with ATP and the pif-pocket ligand RF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XX9
- Type
- protein
- Length
- 289 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
- RF4, ATP
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 289 | 40% helix, 18% strand | O15530 |
Ligands and binding sites
- RF4 · (2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid · ligand · 2 copies · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- GOL · Glycerol · additive · 3 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 | 361 | 0.64 | 0.79 | 37 | ATP |
| 2 | 66 | 0.38 | 0.79 | 23 | empty |
| 3 | 55 | 0.35 | 0.78 | 14 | RF4 |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4XX9 · Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RF4 · 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 4XX9 · PDBe 4XX9 · UniProt O15530
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