Crystal structure of aplysia cyclase complexed with substrate ngd and product cgdpr

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).

Ligands and binding sites

• CGR · Cyclic guanosine diphosphate-ribose · ligand · chains A
• NGD · 3-(aminocarbonyl)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihyd roxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2- yl]pyridinium · ligand · chains B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1488 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

• 3ZWN · Crystal structure of Aplysia cyclase complexed with substrate NGD and product cGDPR · the same entry in another collection · chain A against A, TM-score 1.00
• P29241 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase… · 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 P29241
• Elsewhere: RCSB PDB 3ZWN · PDBe 3ZWN · UniProt P29241