wwPDB validation report of PDB entry 2Q7Y

N-[(1S,2R,3E)-1-({[ALPHA-D-GALACTOPYRANOSYL-(1->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL]OXY}METHYL)-2-H YDROXYHEPTADEC-3-EN-1-YL]OCTANAMIDE

same protein bound to alpha-galactosyl ceramide

same protein bound to microbial alpha-galacturonosyl ceramide

same protein bound to mycobacterial phosphatidylinositol-dimannoside

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

T-cell surface glycoprotein CD1d1, Beta-2-microglobulin
Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d

biologically active unit is a heterodimer of mCD1d and beta2M

The analyses of the Patterson function reveals a significant off-origin peak that is 34.36 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 6.9034e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.

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)