Structure of PDB 6mzb Chain B Binding Site BS01

Receptor Information
>6mzb Chain B (length=807) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FADQYFGRKLSPEDVANACEDGCPEGCTSFRELCQVEESAALFELVQDMQ
ENVNMERVVFKILRRLCSILHADRCSLFMYRQRNGVAELATRLFSVQPDS
VLEDCLVPPDSEIVFPLDIGVVGHVAQTKKMVNVQDVMECPHFSSFADEL
TDYVTRNILATPIMNGKDVVAVIMAVNKLDGPCFTSEDEDVFLKYLNFGT
LNLKIYHLSYLHNCETRRGQVLLWSANKVFEELTDIERQFHKAFYTVRAY
LNCDRYSVGLLDMTKEKEFFDVWPVLMGEAQAYSGPRTPDGREILFYKVI
DYILHGKEDIKVIPSPPADHWALASGLPTYVAESGFICNIMNAPADEMFN
FQEGPLDDSGWIVKNVLSMPIVNKKEEIVGVATFYNRKDGKPFDEQDEVL
MESLTQFLGWSVLNTDTYDKMNKLENRKDIAQDMVLYHVRCDREEIQLIL
PTRERLGKEPADCEEDELGKILKEVLPGPAKFDIYEFHFSDLECTELELV
KCGIQMYYELGVVRKFQIPQEVLVRFLFSVSKGYRRITYHNWRHGFNVAQ
TMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLA
KLHGSSILERHHLEFGKFLLSEETLNIYQNLNRRQHEHVIHLMDIAIIAT
DLALYFKKRTMFQKIVDESKNYEDRKSWVEYLSLETTRKEIVMAMMMTAC
DLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLDQQPIPMMDRNKAAEL
PKLQVGFIDFVCTFVYKEFSRFHEEILPMFDRLQNNRKEWKALADEYEAK
VKALEED
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain6mzb Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6mzb Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		H561 H597
Binding residue
(residue number reindexed from 1)		H544 H580
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6mzb, PDBe:6mzb, PDBj:6mzb
PDBsum6mzb
PubMed30820458
UniProtP23439|PDE6B_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (Gene Name=PDE6B)

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