Structure of PDB 6mzb Chain B Binding Site BS02

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 ID35G
InChIInChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyZOOGRGPOEVQQDX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]4[C@H]3O
ACDLabs 12.01O=C4NC(=Nc1c4ncn1C3OC2COP(=O)(OC2C3O)O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O4)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
FormulaC10 H12 N5 O7 P
NameGUANOSINE-3',5'-MONOPHOSPHATE
ChEMBLCHEMBL395336
DrugBankDB02315
ZINCZINC000004095501
PDB chain6mzb Chain B Residue 903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		R91 S93 F95 F111 G137 V138 V139 F160 S161 M191
Binding residue
(residue number reindexed from 1)		R74 S76 F78 F94 G120 V121 V122 F143 S144 M174
Annotation score4
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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