Structure of PDB 8ugb Chain B

Receptor sequence

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

QVHRFLDQNPGFADQYFGRKLSPEDVANACEDGCPEGCTSFRELCQVEES
AALFELVQDMQENVNMERVVFKILRRLCSILHADRCSLFMYRQRNGVAEL
ATRLFSVQPDSVLEDCLVPPDSEIVFPLDIGVVGHVAQTKKMVNVQDVME
CPHFSSFADELTDYVTRNILATPIMNGKDVVAVIMAVNKLDGPCFTSEDE
DVFLKYLNFGTLNLKIYHLSYLHNCETRRGQVLLWSANKVFEELTDIERQ
FHKAFYTVRAYLNCDRYSVGLLDMTKEKEFFDVWPVLMGEAQAYSGPRTP
DGREILFYKVIDYILHGKEDIKVIPSPPADHWALASGLPTYVAESGFICN
IMNAPADEMFNFQEGPLDDSGWIVKNVLSMPIVNKKEEIVGVATFYNRKD
GKPFDEQDEVLMESLTQFLGWSVLNTDTYDKMNKLENRKDIAQDMVLYHV
RCDREEIQLILPTRERLGKEPADCEEDELGKILKEVLPGPAKFDIYEFHF
SDLECTELELVKCGIQMYYELGVVRKFQIPQEVLVRFLFSVSKGYRRITY
HNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNN
LYQMKSQNPLAKLHGSSILERHHLEFGKFLLSEETLNIYQNLNRRQHEHV
IHLMDIAIIATDLALYFKKRTMFQKIVDESKNYEDRKSWVEYLSLETTRK
EIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLDQQPI
PMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEILPMFDRLQNNRKE
WKALADEYEAK

3D structure

• PDB: 8ugb Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6.
• Chain: B
• 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	B	N101 F111 V124 D127 S128 V131 F132 I136 F163 L167 Y347 G352 F353 I354 C355 M358 N359 V389 E393 E415 E419	N95 F105 V118 D121 S122 V125 F126 I130 F157 L161 Y341 G346 F347 I348 C349 M352 N353 V383 E387 E409 E413
BS02	PCG	B	R91 S93 F111 S112 F132 G137 V138 S161 T168 T172 I175 M191	R85 S87 F105 S106 F126 G131 V132 S155 T162 T166 I169 M185
BS03	ZN	B	H561 H597 D598 D718	H555 H591 D592 D712
BS04	ZUD	B	F740 M758 L767 L770 Q771 F774	F734 M752 L761 L764 Q765 F768

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:0043153 entrainment of circadian clock by photoperiod
• GO:0060041 retina development in camera-type eye

Cellular Component

• GO:0001750 photoreceptor outer segment
• GO:0016020 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: P23439|PDE6B_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (Gene Name=PDE6B)