(quasi-)racemic X-ray crystal structure of glycosylated chemokine ser- CCL1.

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 31% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 27 copies · chains A, D, B, C
• CIT · Citric acid · additive · 2 copies · chains B, C, D

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

5 interfaces between chains.

• A–B · 1102 Ų buried · 10 hydrogen bonds · protein-protein
• C–D · 815 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 235 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
• A–D · 155 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 136 d-amino, 12 disulfide, 2 glycan (D-amino acid, disulfide, N-glycosylation).

Compared structures

• 4OIK · (Quasi-)Racemic X-ray crystal structure of glycosylated chemokine Ser-CCL1. · the same entry in another collection · chain A against A, TM-score 1.00
• P22362 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 1 (P22362) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P22362
• Elsewhere: RCSB PDB 4OIK · PDBe 4OIK · UniProt P22362