Crystal structure of arabidopsis thaliana phosphoserine aminotransferase isoform 1 (ATPSAT1) in complex with pyridoxamine-5'- phosphate (pmp)

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).

Ligands and binding sites

• PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
• NA · Sodium ion · metal · chains B
• SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 2479 Ų buried · 44 hydrogen bonds · protein-protein
• C–D · 2431 Ų buried · 38 hydrogen bonds · protein-protein
• A–D · 249 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 236 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 161 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6CZY · Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1… · the same entry in another collection · chain A against A, TM-score 1.00
• Q96255 · AlphaFold monomer V2.0 prediction for phosphoserine aminotransferase 1, chloroplastic… · a predicted model of the same protein · chain B 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 Q96255
• Elsewhere: RCSB PDB 6CZY · PDBe 6CZY · UniProt Q96255