Research workbench
Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-DICHLOROBENZO[B]THIOPHENE-2- carboxylic acid
Analyse Crystal structure of I170F mutant 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
- 3VAD
- Type
- protein
- Length
- 310 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
- 0F1, ADP, MG, K
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial (EC 2.7.11.4) | protein | 310 | 50% helix, 16% strand | Q00972 |
Ligands and binding sites
- 0F1 · 3,6-dichloro-1-benzothiophene-2-carboxylic acid · ligand · 2 copies · chains A
- ADP · Adenosine-5'-diphosphate · 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 | 97 | 0.77 | 0.97 | 15 | 0F1 |
| 2 | 475 | 0.74 | 0.83 | 59 | ADP, MG, K |
| 3 | 76 | 0.63 | 0.90 | 16 | empty |
| 4 | 53 | 0.29 | 0.75 | 13 | empty |
| 5 | 53 | 0.27 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3VAD · Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in… · 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 3VAD · PDBe 3VAD · UniProt Q00972
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