Crystal structure of ADP-ribosyl cyclase complexed with 8- bromo-ADP-ribose and cyclic 8-bromo-cyclic-ADP-ribose

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 12% strand (DSSP).

Ligands and binding sites

• AV1 · [(2R,3S,4R,5R)-5-(6-amino-8-bromo-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 7 copies · chains A, B, C, E, F, G, H
• CV1 · (2R,3R,4S,5R,13R,14S,15R,16R)-24-amino-18-bromo-3,4,14, 15-tetrahydroxy-7,9,11,25,26-pentaoxa-17,19,22-triaza-1-azonia-8,10-diphosphapentacyclo[18.3.1.1^2,5^.1^13, 16^.0^17,21^]hexacosa-1(24),18,20,22-tetraene-8,10-diolate 8,10-dioxide · ligand · chains D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• E–F · 1512 Ų buried · 21 hydrogen bonds · protein-protein
• A–B · 1498 Ų buried · 25 hydrogen bonds · protein-protein
• C–D · 1486 Ų buried · 20 hydrogen bonds · protein-protein
• G–H · 1442 Ų buried · 15 hydrogen bonds · protein-protein
• B–E · 915 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 disulfide (disulfide).

Compared structures

• 3ZWY · Crystal structure of ADP-ribosyl cyclase complexed with 8-bromo-ADP- ribose and cyclic… · the same entry in another collection · chain H against H, 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 3ZWY · PDBe 3ZWY · UniProt P29241