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Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 1
Analyse Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EAT
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial
- EC
- 2.7.11.2
- UniProt
- Q16654
- Ligands
- W6P, SO4
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (EC 2.7.11.2) | protein | 337 | 58% helix, 15% strand | Q16654 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (EC 2.7.11.2) | protein | 337 | 56% helix, 15% strand | Q16654 |
Ligands and binding sites
- W6P · 1,3-dihydro-2H-indol-2-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.58 | 0.79 | 33 | empty |
| 2 | 85 | 0.52 | 0.84 | 19 | W6P |
| 3 | 94 | 0.51 | 0.83 | 20 | W6P |
| 4 | 86 | 0.40 | 0.77 | 18 | empty |
| 5 | 76 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1497 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7EAT · Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q16654 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 7EAT · PDBe 7EAT · UniProt Q16654
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