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Crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands
Analyse Crystal structures of human pyruvate dehydrogenase kinase 2 containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BU2
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogensae kinase isoenzyme 2
- EC
- 2.7.1.99
- UniProt
- Q15119
- Ligands
- ATP, TF1, MG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogensae kinase isoenzyme 2 (EC 2.7.1.99) | protein | 358 | 51% helix, 15% strand | Q15119 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- TF1 · 4-({(2R,5S)-2,5-dimethyl-4-[(2R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoyl]piperazin-1-yl}carbonyl)benzonitrile · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.67 | 0.88 | 25 | empty |
| 2 | 303 | 0.63 | 0.80 | 32 | ATP, MG |
| 3 | 102 | 0.60 | 0.86 | 14 | TF1 |
| 4 | 125 | 0.45 | 0.77 | 21 | empty |
| 5 | 63 | 0.29 | 0.74 | 10 | empty |
Compared structures
- 2BU2 · crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15119 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q15119
- Elsewhere: RCSB PDB 2BU2 · PDBe 2BU2 · UniProt Q15119
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