Research workbench
X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase
Analyse X-ray structure refinement and comparison of three forms of mitochondrial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9AAT
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P00508
- Ligands
- PMP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate aminotransferase (EC 2.6.1.1) | protein | 401 | 48% helix, 14% strand | P00508 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.74 | 0.79 | 73 | PMP |
| 2 | 737 | 0.73 | 0.79 | 73 | PMP |
| 3 | 147 | 0.61 | 0.85 | 25 | empty |
| 4 | 178 | 0.49 | 0.77 | 34 | empty |
| 5 | 69 | 0.42 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3404 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 9AAT · X-ray structure refinement and comparison of three forms of mitochondrial aspartate… · the same entry in another collection · chain A against A, TM-score 1.00
- P00508 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, mitochondrial (P00508) · 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 P00508
- Elsewhere: RCSB PDB 9AAT · PDBe 9AAT · UniProt P00508
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