The crystal structure of sucrose synthase-1 from arabidopsis thaliana and its functional implications.

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).

Ligands and binding sites

• UDP · Uridine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• FRU · beta-D-fructofuranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
• K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
• SO4 · Sulfate ion · ion · 30 copies · chains A, B, C, D, E, F, G, H
• MLA · Malonic acid · additive · 12 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

13 interfaces between chains.

• E–H · 1348 Ų buried · 13 hydrogen bonds · protein-protein
• B–C · 1344 Ų buried · 12 hydrogen bonds · protein-protein
• A–D · 1325 Ų buried · 12 hydrogen bonds · protein-protein
• F–G · 1316 Ų buried · 14 hydrogen bonds · protein-protein
• G–H · 1168 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

• 3S29 · The crystal structure of sucrose synthase-1 from Arabidopsis thaliana and its functional… · the same entry in another collection · chain H against H, TM-score 1.00
• P49040 · AlphaFold monomer V2.0 prediction for sucrose synthase 1 (P49040) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P49040
• Elsewhere: RCSB PDB 3S29 · PDBe 3S29 · UniProt P49040