Research workbench
Aspartate aminotransferase from saccharomyces cerevisiae cytoplasm
Analyse Aspartate aminotransferase from saccharomyces cerevisiae cytoplasm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YAA
- Type
- protein
- Length
- 1,648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P23542
- Ligands
- MAE, PLP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aspartate aminotransferase (EC 2.6.1.1) | protein | 412 | 46% helix, 14% strand | P23542 |
Ligands and binding sites
- MAE · Maleic acid · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.77 | 0.97 | 29 | MAE, PLP |
| 2 | 104 | 0.77 | 0.97 | 29 | MAE, PLP |
| 3 | 101 | 0.77 | 0.97 | 30 | MAE, PLP |
| 4 | 82 | 0.77 | 0.99 | 26 | empty |
| 5 | 78 | 0.76 | 0.99 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3602 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3560 Ų buried · 63 hydrogen bonds · protein-protein
- A–D · 234 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 156 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1YAA · Aspartate aminotransferase from saccharomyces cerevisiae cytoplasm · the same entry in another collection · chain D against D, TM-score 1.00
- P23542 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, cytoplasmic (P23542) · 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 P23542
- Elsewhere: RCSB PDB 1YAA · PDBe 1YAA · UniProt P23542
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