Crystal structure of human protocadherin 18 EC1-EC4

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 45% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
• FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• CA · Calcium ion · metal · 18 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 8 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1888 Ų buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 6VFR · Crystal structure of human protocadherin 18 EC1-EC4 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HCL0 · AlphaFold monomer V2.0 prediction for protocadherin-18 (Q9HCL0) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q9HCL0
• Elsewhere: RCSB PDB 6VFR · PDBe 6VFR · UniProt Q9HCL0