Research workbench
Crystal structure of E.COLI aspat complexed with N-phosphopyridoxyl-L- glutamic acid
Analyse Crystal structure of E.COLI aspat complexed with N-phosphopyridoxyl-L- glutamic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X28
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P00509
- Ligands
- PGU
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate aminotransferase (EC 2.6.1.1) | protein | 396 | 47% helix, 14% strand | P00509 |
Ligands and binding sites
- PGU · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.79 | 0.96 | 31 | PGU |
| 2 | 147 | 0.78 | 0.96 | 31 | PGU |
| 3 | 314 | 0.55 | 0.75 | 43 | empty |
| 4 | 301 | 0.55 | 0.76 | 49 | empty |
| 5 | 90 | 0.39 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3311 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 1X28 · Crystal Structure of e.coli AspAT complexed with N-phosphopyridoxyl-L-glutamic acid · 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 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 P00509
- Elsewhere: RCSB PDB 1X28 · PDBe 1X28 · UniProt P00509
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