wwPDB validation report of PDB entry 3DZG

Cyclic ADP-ribose hydrolase 1, cADPr hydrolase 1, T10, CD38 antigen

Human CD38 extracellular domain, ara-2-deoxy-2-fluoro-ribose-5'-phosphate complex

Human CD38 extracellular domain, GTP complex

Human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex

Human CD38 extracellular domain E226Q mutant, NMN complex

Human CD38 extracellular domain, NMN complex

AUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM HAVING SP2 HYBRIDIZATION (C1'H) NOT THE SP3 HYBRIDIZATION (C1'H2). AUTHORS ALSO STATE THAT THE PRESENCE OF COVALENT LINK IS THE NATURE OF THE COVALENT REACTION INTERMEDIATE RF5.

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

Crystal structure of human CD38 extracellular domain, ara-F-ribose-5'-phosphate/nicotinamide complex

The largest off-origin peak in the Patterson function is 6.74% of the height of the origin peak. No significant pseudotranslation is detected.

structure factor analysis and validation

geometric validation package for ligand chemistry in protein x-ray structures

20191225.v01 (using entries in the PDB archive December 25th 2019)