wwPDB validation report of PDB entry 3S4Y

hTPK1, Placental protein 20, PP20, Thiamine pyrophosphokinase 1

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. thiamine pyrophosphate restraints were obtained from the prodrg server, using coordinates from pdb entry 2PGN. parrot was used for density modification. Arp/warp and buccaneer were used for automated tracing. Coot was used for interactive model rebuilding and Molprobity was used for geometry validation. CAVEAT: Density for the pyrophosphate moieties of the thiamine pyrophosphate models is poorer than for the protein/ligand model as a whole. Geometry of the moiety is distorted. Anomalous difference fourier density is observed at the pyrophosphate sites. Assignment of the cation near the TPP binding site as calcium is tentative, as coordination geometry deviates from expected ideal configuration. The cation positions are supported by anomalous difference fourier density.

Thiamin pyrophosphokinase 1 (E.C.2.7.6.2)
Crystal structure of human thiamin pyrophosphokinase 1

AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

The largest off-origin peak in the Patterson function is 5.93% of the height of the origin peak. No significant pseudotranslation is detected.

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

structure factor analysis and validation

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