Research workbench
Crystal structure of GABA aminotransferase bound to (S)-3-amino-4- (DIFLUOROMETHYLENYL)CYCLOPENT-1-ene-1-carboxylic acid, an potent inactivatorfor the treatment of addiction
Analyse Crystal structure of GABA aminotransferase bound to (S)-3-amino-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B6G
- Type
- protein
- Length
- 1,847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-aminobutyrate aminotransferase, mitochondrial
- EC
- 2.6.1.19, 2.6.1.22
- UniProt
- P80147
- Ligands
- RMT, FES
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-aminobutyrate aminotransferase, mitochondrial (EC 2.6.1.19, 2.6.1.22) | protein | 461 | 43% helix, 15% strand | P80147 |
| B, C, D | 4-aminobutyrate aminotransferase, mitochondrial (EC 2.6.1.19, 2.6.1.22) | protein | 462 | 44% helix, 14% strand | P80147 |
Ligands and binding sites
- RMT · (3R,4E)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1,3-dicarboxylic acid · ligand · 4 copies · chains A, B, C, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.83 | 0.85 | 114 | FES, RMT |
| 2 | 862 | 0.83 | 0.85 | 111 | FES, RMT, ACT |
| 3 | 83 | 0.76 | 0.98 | 24 | empty |
| 4 | 82 | 0.75 | 0.97 | 20 | empty |
| 5 | 77 | 0.75 | 0.98 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5507 Ų buried · 85 hydrogen bonds · protein-protein
- C–D · 5472 Ų buried · 83 hydrogen bonds · protein-protein
Compared structures
- 6B6G · Crystal Structure of GABA Aminotransferase bound to… · the same entry in another collection · chain D against D, TM-score 1.00
- P80147 · AlphaFold monomer V2.0 prediction for 4-aminobutyrate aminotransferase, mitochondrial… · a predicted model of the same protein · chain C 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 P80147
- Elsewhere: RCSB PDB 6B6G · PDBe 6B6G · UniProt P80147
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