MolNFT v1 · #38917 · protein
Crystal structure of CYS315ALA-CYS318ALA mutant of human mitochondrial branched chain aminotransferase
2HDK · Branched-chain-amino-acid aminotransferase, mitochondrial: “Crystal structure of CYS315ALA-CYS318ALA mutant of human mitochondrial branched chain aminotransferase”. X-ray diffraction, 2 ligands (PLP, COI), 4 pockets (best…
- PDB
- 2HDK
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched-chain-amino-acid aminotransferase, mitochondrial
- EC
- 2.6.1.42
- UniProt
- O15382
- Ligands
- PLP, COI
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Branched-chain-amino-acid aminotransferase, mitochondrial (EC 2.6.1.42) | protein | 363 | 25% helix, 31% strand | O15382 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- COI · 2-oxo-4-methylpentanoic acid · ligand · chains A, B
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.77 | 0.81 | 81 | PLP, COI |
| 2 | 405 | 0.73 | 0.84 | 43 | PLP, ACY |
| 3 | 87 | 0.72 | 0.95 | 41 | empty |
| 4 | 130 | 0.59 | 0.84 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2452 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2HDK · Crystal Structure of Cys315Ala-Cys318Ala Mutant of Human Mitochondrial Branched Chain… · the same entry in another collection · chain A against A, TM-score 1.00
- O15382 · AlphaFold monomer V2.0 prediction for branched-chain-amino-acid aminotransferase… · a predicted model of the same protein · chain B 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 O15382
- Elsewhere: RCSB PDB 2HDK · PDBe 2HDK · UniProt O15382
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