Research workbench
Structural studies reveal the inactivation of E. COLI L-aspartate aminotransferase by (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (sadta) via two mechanisms (at PH6.5)
Analyse Structural studies reveal the inactivation of E. COLI L-aspartate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QA3
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P00509
- Ligands
- PSZ, PMP, SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase (EC 2.6.1.1) | protein | 385 | 47% helix, 14% strand | P00509 |
Ligands and binding sites
- PSZ · 4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]thiophene-2-carboxylic acid · ligand · chains A
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.65 | 0.91 | 18 | PSZ, PMP |
| 2 | 87 | 0.40 | 0.78 | 22 | GOL |
| 3 | 77 | 0.39 | 0.78 | 17 | empty |
| 4 | 51 | 0.34 | 0.79 | 17 | GOL |
| 5 | 75 | 0.33 | 0.75 | 17 | GOL |
Modifications
Observed in the structure: 2 covalent, 1 modified (additive adduct, covalent ligand, nonstandard).
Compared structures
- 2QA3 · Structural Studies Reveal the Inactivation of E. coli L-aspartate aminotransferase by… · the same entry in another collection · chain A against A, TM-score 1.00
- P00509 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase (P00509) · a predicted model of the same protein · chain A 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 P00509
- Elsewhere: RCSB PDB 2QA3 · PDBe 2QA3 · UniProt P00509
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