Research workbench
Crystal structure of branched-chain alpha-ketoacid dehydrogenase KINASE/PHENYLBUTYRATE complex with ADP
Analyse Crystal structure of branched-chain alpha-ketoacid dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TZ5
- Type
- protein
- Length
- 312 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, CLT, MG, K
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial (EC 2.7.11.4) | protein | 312 | 51% helix, 17% strand | Q00972 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CLT · 4-phenyl-butanoic 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
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 | 262 | 0.75 | 0.88 | 32 | ADP, MG, K |
| 2 | 62 | 0.74 | 0.99 | 13 | CLT |
| 3 | 114 | 0.63 | 0.87 | 15 | empty |
| 4 | 191 | 0.47 | 0.75 | 24 | empty |
| 5 | 51 | 0.28 | 0.75 | 13 | empty |
Compared structures
- 3TZ5 · Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate… · 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 0.97
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 Q00972
- Elsewhere: RCSB PDB 3TZ5 · PDBe 3TZ5 · UniProt Q00972
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