4jvf Summary

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The Crystal structure of PDE6D in complex with the inhibitor (s)-5

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 2.4 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 140 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 92%


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 Molecular function (GO) Cellular component (GO) Biological process (GO)
B (O43924) protein bindingsearch GTPase inhibitor activitysearch 3',5'-cyclic-nucleotide phosphodiesterase activitysearch Rab GTPase bindingsearch cytosolsearch membranesearch cytoplasmsearch cytoplasmic vesiclesearch cytoplasmic vesicle membranesearch negative regulation of catalytic activitysearch regulation of GTP catabolic processsearch visual perceptionsearch response to stimulussearch metabolic processsearch

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