Research workbench
Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4
Analyse Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZDY
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase kinase isozyme 4
- EC
- 2.7.11.2
- UniProt
- Q16654
- Ligands
- ADP, MG
- Pockets
- 9 · 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 kinase isozyme 4 (EC 2.7.11.2) | protein | 354 | 53% helix, 14% strand | Q16654 |
| B | Pyruvate dehydrogenase kinase isozyme 4 (EC 2.7.11.2) | protein | 354 | 54% helix, 15% 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
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.74 | 0.82 | 62 | MG, ADP |
| 2 | 478 | 0.71 | 0.81 | 53 | MG, ADP |
| 3 | 315 | 0.61 | 0.79 | 32 | empty |
| 4 | 82 | 0.56 | 0.86 | 15 | empty |
| 5 | 108 | 0.38 | 0.74 | 20 | EPE |
Interfaces
1 interface between chains.
- A–B · 1572 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2ZDY · Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4 · 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 B 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 2ZDY · PDBe 2ZDY · UniProt Q16654
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