Crystal structure of an ALPHA,ALPHA-trehalose-phosphate synthase (udp- forming) from burkholderia xenovorans in complex with glucose-6- phosphate

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 20% strand (DSSP).

Ligands and binding sites

• UDP · Uridine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• OXD · Oxalic acid · ligand · 5 copies · chains A, D, B, C, E, F, G
• G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
• FMT · Formic acid · additive · 27 copies · chains A, E, B, C, D, H, F
• EDO · 1,2-ethanediol · additive · 15 copies · chains A, E, B, F, C, G, D, H
• ACT · Acetate ion · additive · 15 copies · chains A, B, F, C, D, E, G, H
• TAR · D(-)-tartaric acid · additive · chains E

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

12 interfaces between chains.

• D–H · 1303 Ų buried · 15 hydrogen bonds · protein-protein
• B–F · 1284 Ų buried · 16 hydrogen bonds · protein-protein
• C–G · 1276 Ų buried · 13 hydrogen bonds · protein-protein
• A–E · 1268 Ų buried · 17 hydrogen bonds · protein-protein
• A–D · 1117 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5V0T · Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from… · 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 Q13W28
• Elsewhere: RCSB PDB 5V0T · PDBe 5V0T · UniProt Q13W28