Crystal structure of red abalone egg verl repeat 3 in complex with sperm lysin at 1.64 a resolution (crystal form II)

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 27% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
• GLC · alpha-D-glucopyranose · sugar · chains A, B
• FRU · beta-D-fructofuranose · sugar · chains A
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1172 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5IIB · Crystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.64 A… · the same entry in another collection · chain A against A, TM-score 1.00
• P04552 · AlphaFold monomer V2.0 prediction for egg-lysin (P04552) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P04552
• Every structure of UniProt Q8WR62
• Elsewhere: RCSB PDB 5IIB · PDBe 5IIB · UniProt P04552 · UniProt Q8WR62