MolNFT v1 · #93616 · protein
Crystal structure of branched-chain alpha-ketoacid dehydrogenase KINASE/(R)-2-chloro-3-phenylpropanoic acid complex with ADP
4H81 · [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase…: “Crystal structure of branched-chain alpha-ketoacid dehydrogenase KINASE/(R)-2-chloro-3-phenylpropanoic acid…”. X-ray diffraction, 4 ligands (ADP, WJ2, MG), 3 pockets…
- PDB
- 4H81
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
- EC
- 2.7.11.4
- UniProt
- Q00972
- Ligands
- ADP, WJ2, MG, K
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial (EC 2.7.11.4) | protein | 303 | 51% helix, 15% strand | Q00972 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- WJ2 · (2R)-2-chloro-3-phenylpropanoic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.75 | 0.98 | 16 | WJ2 |
| 2 | 519 | 0.72 | 0.80 | 56 | ADP, MG, K |
| 3 | 172 | 0.53 | 0.78 | 16 | empty |
Compared structures
- 4H81 · Crystal structure of branched-chain alpha-ketoacid dehydrogenase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00972 · AlphaFold monomer V2.0 prediction for [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]]… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q00972
- Elsewhere: RCSB PDB 4H81 · PDBe 4H81 · UniProt Q00972
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