MolNFT v1 · #28257 · protein
Crystal structure of the PDK3-L2 complex
1Y8O · [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3: “Crystal structure of the PDK3-L2 complex”. X-ray diffraction, 4 ligands (ADP, RED, K), 4 pockets (best druggability 0.59). MolNFT v1 #28257 on GenesisL1: 3D structure, binding…
- PDB
- 1Y8O
- Type
- protein
- Length
- 471 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
- ADP, RED, K, MG
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 (EC 2.7.1.99) | protein | 374 | 56% helix, 14% strand | Q15120 |
| B | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 97 | 7% helix, 40% strand | P10515 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.59 | 0.83 | 21 | RED |
| 2 | 274 | 0.57 | 0.77 | 30 | empty |
| 3 | 203 | 0.55 | 0.79 | 27 | MG, K, ADP |
| 4 | 191 | 0.48 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 498 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1Y8O · 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 1Y8O · PDBe 1Y8O · UniProt Q15120 · UniProt P10515
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