Crystal structure of ternary complex of plasmodium vivax shmt with D- serine and folinic acid

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).

Ligands and binding sites

• 1W9 · (2R)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanyl-propanoic acid · ligand · 3 copies · chains A, B, C
• FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · 3 copies · chains A, B, C
• GOL · Glycerol · additive · 3 copies · chains A, B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
• ETF · Trifluoroethanol · additive · chains C

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

Pockets

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

Interfaces

2 interfaces between chains.

• A–B · 4694 Ų buried · 61 hydrogen bonds · protein-protein
• B–C · 402 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 4OYT · Crystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic… · the same entry in another collection · 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 A5K8L9
• Elsewhere: RCSB PDB 4OYT · PDBe 4OYT · UniProt A5K8L9