Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 2 (ATMAT2) in complex with S-adenosylmethionine and ppnp

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).

Ligands and binding sites

• PPK · (diphosphono)aminophosphonic acid · ligand · 2 copies · chains A, B
• SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 4 copies · chains A, B
• K · Potassium ion · metal · 2 copies · chains A, B
• MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, B
• PGE · Triethylene glycol · additive · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
• 1PE · Pentaethylene glycol · additive · chains A
• PDO · 1,3-propandiol · additive · chains B
• PGR · R-1,2-propanediol · additive · chains B
• PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3048 Ų buried · 46 hydrogen bonds · protein-protein

Compared structures

• 6VD1 · Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in… · the same entry in another collection · chain A against A, TM-score 1.00
• P17562 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase 2 (P17562) · a predicted model of the same protein · chain B 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 P17562
• Elsewhere: RCSB PDB 6VD1 · PDBe 6VD1 · UniProt P17562