4jv8 Summary


The crystal structure of PDE6D in complex with rac-S1

The structure was published by Zimmermann, G., Papke, B., Ismail, S., et al., Wittinghofer, A., Bastiaens, P.I., and Waldmann, H., in 2013 in a paper entitled "Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.45 Å and deposited in 2013.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta. This molecule has the UniProt identifier O43924 (PDE6D_HUMAN)search. The sample contained 152 residues which is 100% of the natural sequence. Out of 152 residues 145 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):

Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
B Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta O43924 (1-150) (PDE6D_HUMAN)search Homo sapienssearch 100% 152 96%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
O43924 (1 - 150) Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Homo sapiens

Chain Sequence family (Pfam)
B (O43924) PF05351: GMP-PDE, delta subunitsearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
B (O43924) visual perceptionsearch metabolic processsearch response to stimulussearch negative regulation of catalytic activitysearch organelle organizationsearch protein bindingsearch 3',5'-cyclic-nucleotide phosphodiesterase activitysearch GTPase inhibitor activitysearch Rab GTPase bindingsearch membranesearch cytoplasmic vesiclesearch primary ciliumsearch cytoplasmsearch cytosolsearch cell projectionsearch cytoplasmic vesicle membranesearch cytoskeletonsearch

Chain InterPro annotation
B GMP phosphodiesterase, delta subunitsearch Immunoglobulin E-setsearch Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunitsearch