Crystal structure of the glycophorin a transmembrane dimer in lipidic cubic phase

Structure

x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).

Ligands and binding sites

• OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · chains A, B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–D · 492 Ų buried · 0 hydrogen bonds · protein-protein
• C–D · 456 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 452 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 193 Ų buried · 2 hydrogen bonds · protein-protein
• B–D · 144 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation).

Compared structures

• 5EH4 · Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase · the same entry in another collection · chain A against A, TM-score 1.00
• P02724 · AlphaFold monomer V2.0 prediction for glycophorin-a (P02724) · a predicted model of the same protein · chain A against A, TM-score 0.76

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 P02724
• Elsewhere: RCSB PDB 5EH4 · PDBe 5EH4 · UniProt P02724