Crystal structure of the human rage ectodomain (VC1C2 fragment) in complex with human S100A6

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).

Ligands and binding sites

• ZN · Zinc ion · metal · 7 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains B
• CL · Chloride ion · ion · 5 copies · chains A, B
• ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 460 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 4YBH · Crystal structure of the human RAGE ectodomain (VC1C2 fragment) in complex with human… · the same entry in another collection · chain A against A, TM-score 1.00
• P06703 · AlphaFold monomer V2.0 prediction for protein S100-A6 (P06703) · a predicted model of the same protein · chain B against A, TM-score 0.92
• Q15109 · AlphaFold monomer V2.0 prediction for advanced glycosylation end product-specific… · a predicted model of the same protein · chain A against A, TM-score 0.77

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 Q15109
• Every structure of UniProt P06703
• Elsewhere: RCSB PDB 4YBH · PDBe 4YBH · UniProt Q15109 · UniProt P06703