Crystal structure of platelet factor 4 complexed with fondaparinux

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).

Ligands and binding sites

• ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · chains B
• SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains A, B
• IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains A, B
• BDP · beta-D-glucopyranuronic acid · sugar · chains A
• SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A

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

Interfaces

1 interface between chains.

• A–B · 818 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 4R9W · Crystal structure of platelet factor 4 complexed with fondaparinux · the same entry in another collection · chain A against A, TM-score 1.00
• P02776 · AlphaFold monomer V2.0 prediction for platelet factor 4 (P02776) · 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 P02776
• Elsewhere: RCSB PDB 4R9W · PDBe 4R9W · UniProt P02776