Research workbench
Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP
Analyse Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2R
- Type
- protein
- Length
- 716 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
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 4 (EC 2.7.11.2) | protein | 354 | 55% helix, 15% strand | Q16654 |
| B | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 4 (EC 2.7.11.2) | protein | 362 | 52% 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
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.74 | 0.81 | 68 | MG, ADP |
| 2 | 487 | 0.71 | 0.80 | 57 | MG, ADP |
| 3 | 320 | 0.60 | 0.78 | 34 | empty |
| 4 | 87 | 0.58 | 0.86 | 15 | empty |
| 5 | 362 | 0.56 | 0.74 | 55 | GOL |
Interfaces
1 interface between chains.
- A–B · 1909 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3D2R · Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP · 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 3D2R · PDBe 3D2R · UniProt Q16654
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