MolNFT v1 · #31538 · protein
Aromatic amino acid aminotransferase with 5-phenylvaleric acid
2AY9: “Aromatic amino acid aminotransferase with 5-phenylvaleric acid”. X-ray diffraction, 2 ligands (PLP, 5PV), 12 pockets (best druggability 0.77). MolNFT v1 #31538 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2AY9
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic amino acid aminotransferase
- EC
- 2.6.1.57
- UniProt
- P95468
- Ligands
- PLP, 5PV
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic amino acid aminotransferase (EC 2.6.1.57) | protein | 394 | 51% helix, 14% strand | P95468 |
| B | Aromatic amino acid aminotransferase (EC 2.6.1.57) | protein | 388 | 50% helix, 13% strand | P95468 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 5PV · 5-phenylvaleric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.77 | 0.95 | 33 | PLP, 5PV |
| 2 | 497 | 0.71 | 0.80 | 52 | PLP, 5PV |
| 3 | 67 | 0.68 | 0.94 | 24 | empty |
| 4 | 107 | 0.51 | 0.82 | 31 | empty |
| 5 | 106 | 0.44 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3577 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2AY9 · Aromatic amino acid aminotransferase with 5-phenylvaleric acid · the same entry in another collection · chain A against A, TM-score 1.00
- P95468 · AlphaFold monomer V2.0 prediction for aromatic-amino-acid aminotransferase (P95468) · 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 P95468
- Elsewhere: RCSB PDB 2AY9 · PDBe 2AY9 · UniProt P95468
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