MolNFT v1 · #110553 · protein
Gamma-aminobutyric acid aminotransferase inactivated by (1S,3S)-3- amino-4-difluoromethylenyl-1-cyclopentanoic acid (cpp-115)
4Y0D · 4-aminobutyrate aminotransferase, mitochondrial: “Gamma-aminobutyric acid aminotransferase inactivated by (1S,3S)-3…”. X-ray diffraction, 2 ligands (RW2, FES), 20 pockets (best druggability 0.78). MolNFT v1 #110553 on GenesisL1: 3D…
- PDB
- 4Y0D
- Type
- protein
- Length
- 1,846 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
- RW2, FES
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4-aminobutyrate aminotransferase, mitochondrial (EC 2.6.1.19, 2.6.1.22) | protein | 462 | 43% helix, 15% strand | P80147 |
| B, D | 4-aminobutyrate aminotransferase, mitochondrial (EC 2.6.1.19, 2.6.1.22) | protein | 461 | 43% helix, 14% strand | P80147 |
Ligands and binding sites
- RW2 · (1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-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
- GOL · Glycerol · additive · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.78 | 0.88 | 62 | FES, RW2 |
| 2 | 379 | 0.77 | 0.87 | 54 | RW2 |
| 3 | 407 | 0.77 | 0.86 | 53 | RW2 |
| 4 | 419 | 0.76 | 0.86 | 55 | RW2 |
| 5 | 78 | 0.75 | 0.98 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5473 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 5468 Ų buried · 80 hydrogen bonds · protein-protein
Compared structures
- P80147 · AlphaFold monomer V2.0 prediction for 4-aminobutyrate aminotransferase, mitochondrial… · a predicted model of the same protein · chain D 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 4Y0D · PDBe 4Y0D · UniProt P80147
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