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X-ray crystal structure at 1.81A resolution of human mitochondrial branched chain aminotransferase (bcatm) complexed with an aryl acetate compound and an internal aldimine linked plp cofactor.
Analyse X-ray crystal structure at 1.81A 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
- 5I5Y
- Type
- protein
- Length
- 722 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, 68D, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% 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 | 359 | 25% helix, 31% strand | O15382 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 68D · {2-[(5-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carbonyl)amino]phenyl}acetic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.77 | 0.82 | 77 | PLP, 68D, EDO |
| 2 | 135 | 0.75 | 0.94 | 41 | empty |
| 3 | 455 | 0.74 | 0.83 | 51 | PLP, 68D |
| 4 | 139 | 0.61 | 0.85 | 28 | CL |
| 5 | 74 | 0.38 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2375 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I5Y · X-ray crystal structure at 1.81A 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 5I5Y · PDBe 5I5Y · UniProt O15382
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