Research workbench
Crystal structure of aspat from corynebacterium glutamicum
Analyse Crystal structure of aspat from corynebacterium glutamicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HXX
- Type
- protein
- Length
- 847 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- A0A0J9X1V2
- Ligands
- PMP, AKG, PLP, GLU
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase (EC 2.6.1.1) | protein | 424 | 46% helix, 14% strand | A0A0J9X1V2 |
| B | Aspartate aminotransferase (EC 2.6.1.1) | protein | 423 | 45% helix, 14% strand | A0A0J9X1V2 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A, B
- AKG · 2-oxoglutaric acid · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- GLU · Glutamic acid · ligand · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.82 | 0.96 | 43 | empty |
| 2 | 65 | 0.74 | 0.99 | 22 | empty |
| 3 | 227 | 0.70 | 0.87 | 40 | PLP, GLU |
| 4 | 205 | 0.67 | 0.85 | 33 | PMP, AKG |
| 5 | 58 | 0.26 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2551 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5HXX · Crystal structure of AspAT from Corynebacterium glutamicum · the same entry in another collection · chain B against B, 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 A0A0J9X1V2
- Elsewhere: RCSB PDB 5HXX · PDBe 5HXX · UniProt A0A0J9X1V2
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