Crystal structure of red kidney bean purple acid phosphatase in complex with maybridge fragment CC27209

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 29% strand (DSSP).

Ligands and binding sites

• 0LV · (2,2-dimethyl-2,3-dihydro-1-benzofuran-7-yl)methanol · ligand · 4 copies · chains A, D, B, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, B, D
• FUC · alpha-L-fucopyranose · sugar · 9 copies · chains C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
• GOL · Glycerol · additive · 3 copies · chains A, D, B, C
• ACT · Acetate ion · additive · chains A
• EDO · 1,2-ethanediol · additive · chains A

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

Pockets

16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–D · 1566 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 1518 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 497 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 495 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 4DT2 · Crystal structure of red kidney bean purple acid phosphatase in complex with Maybridge… · 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 O24319
• Elsewhere: RCSB PDB 4DT2 · PDBe 4DT2 · UniProt O24319