P-selectin LECTIN/EGF domains complexed with psgl-1 peptide

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 32% strand (DSSP).

Ligands and binding sites

• GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, C, A, D
• NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, C, A, D
• SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains B, A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, A
• SR · Strontium ion · metal · 2 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains B, C
• MRD · (4R)-2-methylpentane-2,4-diol · additive · 7 copies · chains A, B

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

3 interfaces between chains.

• A–D · 439 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 429 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 243 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 5 modified, 2 glycan (disulfide, sulfation, O-glycosylation).

Compared structures

• 1G1S · P-selectin LECTIN/EGF domains complexed with psgl-1 peptide · the same entry in another collection · chain D against D, TM-score 1.00
• P16109 · AlphaFold monomer V2.0 prediction for P-selectin (P16109) · a predicted model of the same protein · chain B against A, TM-score 0.80
• Q14242 · AlphaFold monomer V2.0 prediction for P-selectin glycoprotein ligand 1 (Q14242) · a predicted model of the same protein · chain D against A, TM-score 0.27

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 P16109
• Every structure of UniProt Q14242
• Elsewhere: RCSB PDB 1G1S · PDBe 1G1S · UniProt P16109 · UniProt Q14242