Research workbench
Pyruvate dehydrogenase kinase, isozyme 2, containing ADP
Analyse Pyruvate dehydrogenase kinase, isozyme 2, containing ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JM6
- Type
- protein
- Length
- 675 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase kinase, isozyme 2
- EC
- 2.7.1.99
- UniProt
- Q64536
- Ligands
- ADP, MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase kinase, isozyme 2 (EC 2.7.1.99) | protein | 339 | 50% helix, 15% strand | Q64536 |
| B | Pyruvate dehydrogenase kinase, isozyme 2 (EC 2.7.1.99) | protein | 336 | 51% helix, 15% strand | Q64536 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.75 | 0.87 | 36 | MG, ADP |
| 2 | 253 | 0.73 | 0.87 | 33 | MG, ADP |
| 3 | 338 | 0.66 | 0.80 | 34 | empty |
| 4 | 184 | 0.50 | 0.77 | 23 | empty |
| 5 | 135 | 0.49 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1164 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1JM6 · Pyruvate dehydrogenase kinase, isozyme 2, containing ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q64536 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q64536
- Elsewhere: RCSB PDB 1JM6 · PDBe 1JM6 · UniProt Q64536
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