Research workbench
Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol
Analyse Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q8I
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3; Dihydrolipoyllysine-residue…
- EC
- 2.7.11.2, 2.3.1.12
- UniProt
- Q15120, P10515
- Ligands
- RDC, RED, K
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 (EC 2.7.11.2) | protein | 369 | 54% helix, 14% strand | Q15120 |
| B | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 93 | 6% helix, 42% strand | P10515 |
Ligands and binding sites
- RDC · Radicicol · ligand · chains A
- RED · Dihydrolipoic acid · ligand · chains A, B
- K · Potassium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.58 | 0.84 | 14 | RED |
| 2 | 300 | 0.57 | 0.76 | 35 | empty |
| 3 | 225 | 0.53 | 0.77 | 27 | RDC |
| 4 | 124 | 0.41 | 0.75 | 23 | empty |
| 5 | 53 | 0.31 | 0.76 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Q8I · Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol · the same entry in another collection · chain A against A, TM-score 1.00
- Q15120 · 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
- P10515 · AlphaFold monomer V2.0 prediction for dihydrolipoyllysine-residue acetyltransferase… · 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 Q15120
- Every structure of UniProt P10515
- Elsewhere: RCSB PDB 2Q8I · PDBe 2Q8I · UniProt Q15120 · UniProt P10515
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