Decameric crystal structure of human serum amyloid P-component bound to bis-1,2-{[(Z)-2CARBOXY- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}- piperazine

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Ligands and binding sites

• CPK · Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbonyl}-piperazine · ligand · 3 copies · chains D, I, C, J, E, H
• CA · Calcium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

18 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

14 interfaces between chains.

• F–J · 801 Ų buried · 9 hydrogen bonds · protein-protein
• A–E · 797 Ų buried · 10 hydrogen bonds · protein-protein
• G–H · 793 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 788 Ų buried · 8 hydrogen bonds · protein-protein
• F–G · 784 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

• 2A3X · Decameric crystal structure of human serum amyloid P-component bound to… · the same entry in another collection · chain J against J, TM-score 1.00
• P02743 · AlphaFold monomer V2.0 prediction for serum amyloid P-component (P02743) · a predicted model of the same protein · chain A 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 P02743
• Elsewhere: RCSB PDB 2A3X · PDBe 2A3X · UniProt P02743