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X-ray crystal structure at 2.40A resolution of human mitochondrial branched chain aminotransferase (bcatm) complexed with a tetrahydronaphthalenyl compound and an internal aldimine linked plp cofactor.
Analyse X-ray crystal structure at 2.40A resolution of human mitochondrial branched… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I5U
- Type
- protein
- Length
- 723 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.404
- Source
- Homo sapiens
- Molecule
- Branched-chain-amino-acid aminotransferase, mitochondrial
- EC
- 2.6.1.42
- UniProt
- O15382
- Ligands
- PLP, 67Y, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.404 · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain-amino-acid aminotransferase, mitochondrial (EC 2.6.1.42) | protein | 363 | 25% helix, 31% strand | O15382 |
| B | Branched-chain-amino-acid aminotransferase, mitochondrial (EC 2.6.1.42) | protein | 360 | 24% helix, 31% strand | O15382 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 67Y · 2-hydroxy-N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]acetamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 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 | 133 | 0.79 | 0.97 | 30 | PLP, 67Y |
| 2 | 305 | 0.75 | 0.87 | 47 | PLP, 67Y |
| 3 | 168 | 0.70 | 0.89 | 47 | empty |
| 4 | 217 | 0.58 | 0.79 | 31 | empty |
| 5 | 156 | 0.52 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2398 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I5U · X-ray crystal structure at 2.40A resolution 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 5I5U · PDBe 5I5U · UniProt O15382
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