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X-ray crystal structure at 2.06A resolution of human mitochondrial branched chain aminotransferase (bcatm) complexed with a benzisoxazole compound and an internal aldimine linked plp cofactor.
Analyse X-ray crystal structure at 2.06A 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
- 5I5S
- 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, NVU, CL
- Pockets
- 5 · best druggability 0.77
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 | 361 | 25% helix, 31% strand | O15382 |
| B | Branched-chain-amino-acid aminotransferase, mitochondrial (EC 2.6.1.42) | protein | 356 | 25% helix, 32% strand | O15382 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NVU · 2-(1,2-benzoxazol-3-yl)ethanoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.77 | 0.85 | 67 | PLP, NVU |
| 2 | 311 | 0.75 | 0.87 | 46 | PLP, NVU |
| 3 | 157 | 0.68 | 0.88 | 52 | EDO |
| 4 | 185 | 0.55 | 0.79 | 29 | empty |
| 5 | 69 | 0.30 | 0.74 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 2384 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I5S · X-ray crystal structure at 2.06A 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 1.00
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 5I5S · PDBe 5I5S · UniProt O15382
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