Research workbench
Crystal structure of reduced human cytosolic branched-chain aminotransferase complexed with gabapentin
Analyse Crystal structure of reduced human cytosolic branched-chain aminotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2COJ
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched chain aminotransferase 1, cytosolic
- EC
- 2.6.1.42
- UniProt
- P54687
- Ligands
- PLP, GBN, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched chain aminotransferase 1, cytosolic (EC 2.6.1.42) | protein | 359 | 25% helix, 31% strand | P54687 |
| B | Branched chain aminotransferase 1, cytosolic (EC 2.6.1.42) | protein | 358 | 25% helix, 30% strand | P54687 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GBN · [1-(aminomethyl)cyclohexyl]acetic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.82 | 0.97 | 29 | PLP, GBN |
| 2 | 155 | 0.81 | 0.97 | 30 | PLP, GBN |
| 3 | 79 | 0.65 | 0.92 | 25 | empty |
| 4 | 208 | 0.59 | 0.81 | 34 | empty |
| 5 | 142 | 0.54 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2487 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2COJ · Crystal structure of reduced human cytosolic branched-chain aminotransferase complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P54687 · 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 P54687
- Elsewhere: RCSB PDB 2COJ · PDBe 2COJ · UniProt P54687
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