Crystal complex of N-terminal sucrase-isomaltase with kotalanol

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).

Ligands and binding sites

• KTL · (1S,2R,3R,4S)-1-{(1S)-2-[(2R,3S,4S)-3,4-dihydroxy-2-(hydroxymethyl)tetrahydrothiophenium-1-yl]-1-hydroxyethyl}-2,3,4,5-tetrahydroxypentyl sulfate · ligand · 2 copies · chains B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
• BMA · beta-D-mannopyranose · sugar · 3 copies
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• CL · Chloride ion · ion · chains A
• PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• B–C · 853 Ų buried · 9 hydrogen bonds · protein-protein
• A–B · 488 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 147 Ų buried · 1 hydrogen bond · protein-protein
• C–D · 111 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 11 glycan (disulfide, N-glycosylation).

Compared structures

• 3LPP · Crystal complex of N-terminal sucrase-isomaltase with kotalanol · the same entry in another collection · chain A against A, TM-score 1.00
• P14410 · AlphaFold monomer V2.0 prediction for sucrase-isomaltase, intestinal (P14410) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 P14410
• Elsewhere: RCSB PDB 3LPP · PDBe 3LPP · UniProt P14410