Crystal structure of calcium and zinc-bound human S100A8 in space group C2221

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 2% strand (DSSP).

Ligands and binding sites

• CA · Calcium ion · metal · 8 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 8 copies · chains A, C, D, B
• CL · Chloride ion · ion · 8 copies · chains A, C, D, B
• ACT · Acetate ion · additive · 4 copies · chains A, B, D
• CAC · Cacodylate ion · additive · 2 copies · chains A, C, B, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–D · 1314 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 1310 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 298 Ų buried · 3 hydrogen bonds · protein-protein
• C–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
• A–D · 148 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5HLO · Crystal structure of calcium and zinc-bound human S100A8 in space group C2221 · the same entry in another collection · chain A against A, TM-score 1.00
• P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P05109
• Elsewhere: RCSB PDB 5HLO · PDBe 5HLO · UniProt P05109