MolNFT v1 · #121172 · protein
X-ray crystal structure of human mitochondrial branched chain aminotransferase (bcatm) complexed with a 2-aryl benzimidazole compound and an internal aldimine linked plp cofactor
5HNE · Branched-chain-amino-acid aminotransferase, mitochondrial: “X-ray crystal structure of human mitochondrial branched chain aminotransferase (bcatm) complexed with a…”. X-ray diffraction, 3 ligands (PLP, EL2, CL), 7 pockets (best…
- PDB
- 5HNE
- Type
- protein
- Length
- 717 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, EL2, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain-amino-acid aminotransferase, mitochondrial (EC 2.6.1.42) | protein | 359 | 25% helix, 31% strand | O15382 |
| B | Branched-chain-amino-acid aminotransferase, mitochondrial (EC 2.6.1.42) | protein | 358 | 25% helix, 32% strand | O15382 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- EL2 · 1-[(1R,3S)-3-{[(5-bromothiophen-2-yl)carbonyl]amino}cyclohexyl]-N-methyl-2-(pyridin-2-yl)-1H-benzimidazole-5-carboxamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.76 | 0.96 | 39 | EDO |
| 2 | 441 | 0.74 | 0.83 | 54 | PLP, EL2 |
| 3 | 438 | 0.73 | 0.83 | 55 | PLP, EL2 |
| 4 | 193 | 0.60 | 0.81 | 28 | empty |
| 5 | 165 | 0.57 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2392 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5HNE · X-ray crystal structure of human mitochondrial branched chain aminotransferase (bcatm)… · 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 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 O15382
- Elsewhere: RCSB PDB 5HNE · PDBe 5HNE · UniProt O15382
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