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Crystal structure of mouse mitochondrial aspartate aminotransferase in complex with oxaloacetic acid
Analyse Crystal structure of mouse mitochondrial aspartate aminotransferase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PDB
- Type
- protein
- Length
- 1,604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase, mitochondrial
- EC
- 2.6.1.1
- UniProt
- P05202
- Ligands
- PMP, OAA
- Pockets
- 20 · 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, C, D | Aspartate aminotransferase, mitochondrial (EC 2.6.1.1) | protein | 401 | 48% helix, 14% strand | P05202 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B, C, D
- OAA · Oxaloacetate ion · ligand · chains A, B
- BME · Beta-mercaptoethanol · additive · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.74 | 0.79 | 83 | BME, PMP |
| 2 | 650 | 0.72 | 0.79 | 59 | BME, PMP |
| 3 | 583 | 0.68 | 0.78 | 43 | OAA |
| 4 | 535 | 0.68 | 0.78 | 46 | BME |
| 5 | 196 | 0.63 | 0.84 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3314 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3293 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 3PDB · Crystal structure of mouse mitochondrial aspartate aminotransferase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P05202 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, mitochondrial (P05202) · a predicted model of the same protein · chain A 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 P05202
- Elsewhere: RCSB PDB 3PDB · PDBe 3PDB · UniProt P05202
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