Structure of PDB 8ugb Chain A

Receptor sequence

>8ugbA (length=811) Species: 9913 (Bos taurus)

EEVEKFLDSNVSFAKQYYNLRYRAKVISDLLGPREAAVDFSNYHALNSVE
ESEIIFDLLRDFQDNLQAEKCVFNVMKKLCFLLQADRMSLFMYRARNGIA
ELATRLFNVHKDAVLEECLVAPDSEIVFPLDMGVVGHVALSKKIVNVPNT
EEDEHFCDFVDTLTEYQTKNILASPIMNGKDVVAIIMVVNKVDGPHFTEN
DEEILLKYLNFANLIMKVFHLSYLHNCETRRGQILLWSGSKVFEELTDIE
RQFHKALYTVRAFLNCDRYSVGLLDMTKQKEFFDVWPVLMGEAPPYAGPR
TPDGREINFYKVIDYILHGKEDIKVIPNPPPDHWALVSGLPTYVAQNGLI
CNIMNAPSEDFFAFQKEPLDESGWMIKNVLSMPIVNKKEEIVGVATFYNR
KDGKPFDEMDETLMESLTQFLGWSVLNPDTYELMNKLENRKDIFQDMVKY
HVKCDNEEIQTILKTREVYGKEPWECEEEELAEILQGELPDADKYEINKF
HFSDLPLTELELVKCGIQMYYELKVVDKFHIPQEALVRFMYSLSKGYRRI
TYHNWRHGFNVGQTMFSLLVTGKLKRYFTDLEALAMVTAAFCHDIDHRGT
NNLYQMKSQNPLAKLHGSSILERHHLEFGKTLLRDESLNIFQNLNRRQHE
HAIHMMDIAIIATDLALYFKKRTMFQKIVDQSKTYETQQEWTQYMMLDQT
RKEIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLQQN
PIPMMDRNKADELPKLQVGFIDFVCTFVYKEFSRFHEEITPMLDGITNNR
KEWKALADEYE

3D structure

• PDB: 8ugb Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6.
• Chain: A
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	A	N103 F113 P128 D129 S130 E131 I132 V133 D137 M138 F165 L169 T170 E171 Y349 G354 L355 I356 C357 M360 N361 V391	N97 F107 P122 D123 S124 E125 I126 V127 D131 M132 F159 L163 T164 E165 Y343 G348 L349 I350 C351 M354 N355 V385
BS02	PCG	A	S95 F97 F113 N114 F134 V140 V141 C163 V166 T170 Y172 M193 V195	S89 F91 F107 N108 F128 V134 V135 C157 V160 T164 Y166 M187 V189
BS03	ZN	A	H563 H599 D600 D720	H557 H593 D594 D714
BS04	ZUD	A	M760 L772 Q773 F776	M754 L766 Q767 F770

Gene Ontology

Molecular Function

• GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
• GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity
• GO:0004117 calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding
• GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity
• GO:0048101 calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity

Biological Process

• GO:0007165 signal transduction
• GO:0007601 visual perception
• GO:0019933 cAMP-mediated signaling
• GO:0060041 retina development in camera-type eye

Cellular Component

• GO:0001750 photoreceptor outer segment
• GO:0005886 plasma membrane
• GO:0042622 photoreceptor outer segment membrane
• GO:0042995 cell projection
• GO:0097381 photoreceptor disc membrane

External links

• PDB: RCSB:8ugb, PDBe:8ugb, PDBj:8ugb
• PDBsum: 8ugb
• PubMed: 38159849
• UniProt: P11541|PDE6A_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (Gene Name=PDE6A)