Research workbench
Crystal structure of branched-chain alpha-ketoacid dehydrogenase KINASE/(S)-2-chloro-3-phenylpropanoic acid complex with amppnp
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
- 4E02
- Type
- protein
- Length
- 307 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
- ANP, WJ1, K, MG
- 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 | 307 | 51% helix, 15% strand | Q00972 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- WJ1 · (S)-2-chloro-3-phenylpropanoic acid · ligand · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium 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 | 69 | 0.75 | 0.98 | 14 | WJ1 |
| 2 | 506 | 0.71 | 0.80 | 55 | ANP, K, MG |
| 3 | 89 | 0.59 | 0.87 | 13 | empty |
Compared structures
- 4E02 · 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 0.98
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 4E02 · PDBe 4E02 · UniProt Q00972
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