MolNFT v1 · #56614 · protein
Crystal structure of human PDK4-ADP complex
2ZKJ · [pyruvate dehydrogenase [lipoamide]] kinase isozyme 4: “Crystal structure of human PDK4-ADP complex”. X-ray diffraction, 3 ligands (ADP, MG, PO4), 7 pockets (best druggability 0.74). MolNFT v1 #56614 on GenesisL1: 3D structure…
- PDB
- 2ZKJ
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase [lipoamide]] kinase isozyme 4
- EC
- 2.7.11.2
- UniProt
- Q16654
- Ligands
- ADP, MG, PO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 4 (EC 2.7.11.2) | protein | 355 | 55% helix, 15% strand | Q16654 |
| B | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 4 (EC 2.7.11.2) | protein | 359 | 51% helix, 14% strand | Q16654 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.74 | 0.81 | 63 | MG, ADP, PO4 |
| 2 | 514 | 0.73 | 0.81 | 57 | MG, ADP, PO4 |
| 3 | 310 | 0.62 | 0.79 | 37 | empty |
| 4 | 86 | 0.56 | 0.85 | 15 | empty |
| 5 | 192 | 0.48 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1795 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
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 Q16654
- Elsewhere: RCSB PDB 2ZKJ · PDBe 2ZKJ · UniProt Q16654
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