Research workbench
Crystal structure of the PDK3-L2 complex
Analyse Crystal structure of the PDK3-L2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y8P
- Type
- protein
- Length
- 478 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
- 2.7.1.99, 2.3.1.12
- UniProt
- Q15120, P10515
- Ligands
- ATP, RED, K, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 (EC 2.7.1.99) | protein | 381 | 52% helix, 13% strand | Q15120 |
| B | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 97 | 3% helix, 40% strand | P10515 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- RED · Dihydrolipoic acid · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 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 | 503 | 0.72 | 0.81 | 59 | MG, ATP |
| 2 | 125 | 0.59 | 0.84 | 15 | RED |
| 3 | 334 | 0.59 | 0.77 | 43 | K |
| 4 | 59 | 0.38 | 0.79 | 13 | empty |
| 5 | 70 | 0.27 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1Y8P · Crystal structure of the PDK3-L2 complex · 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 0.94
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 1Y8P · PDBe 1Y8P · UniProt Q15120 · UniProt P10515
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