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Sambucus nigra agglutinin II, tetragonal crystal form- complexed to lactose

Analyse Sambucus nigra agglutinin II, tetragonal crystal form- complexed to lactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3CA4
Type
protein
Length
257 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Agglutinin II
UniProt
P33183
Ligands
NAG, FUC, BGC, GAL, SO4
Pockets
1 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 37% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAgglutinin IIprotein25713% helix, 37% strandP33183

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
  • FUC · alpha-L-fucopyranose · sugar · 2 copies
  • BGC · beta-D-glucopyranose · sugar · 2 copies · chains A
  • GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
  • SO4 · Sulfate ion · ion · 6 copies · chains A
  • ACT · Acetate ion · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11080.440.7818empty

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

  • 3CA4 · Sambucus nigra agglutinin II, tetragonal crystal form- complexed to lactose · the same entry in another collection · chain A against A, TM-score 1.00
  • P33183 · AlphaFold monomer V2.0 prediction for nigrin B (P33183) · a predicted model of the same protein · chain A against A, TM-score 0.99

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