Structure of PDB 6mzb Chain A Binding Site BS02

Receptor Information
>6mzb Chain A (length=820) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVEKFLDSNVSFAKQYYNLRYRAKVISDLLGPREAAVDFSNYHALNSVEE
SEIIFDLLRDFQDNLQAEKCVFNVMKKLCFLLQADRMSLFMYRARNGIAE
LATRLFNVHKDAVLEECLVAPDSEIVFPLDMGVVGHVALSKKIVNVPNTE
EDEHFCDFVDTLTEYQTKNILASPIMNGKDVVAIIMVVNKVDGPHFTEND
EEILLKYLNFANLIMKVFHLSYLHNCETRRGQILLWSGSKVFEELTDIER
QFHKALYTVRAFLNCDRYSVGLLDMTKQKEFFDVWPVLMGEAPPYAGPRT
PDGREINFYKVIDYILHGKEDIKVIPNPPPDHWALVSGLPTYVAQNGLIC
NIMNAPSEDFFAFQKEPLDESGWMIKNVLSMPIVNKKEEIVGVATFYNRK
DGKPFDEMDETLMESLTQFLGWSVLNPDTYELMNKLENRKDIFQDMVKYH
VKCDNEEIQTILKTREVYGKEPWECEEEELAEILQGELPDADKYEINKFH
FSDLPLTELELVKCGIQMYYELKVVDKFHIPQEALVRFMYSLSKGYRRIT
YHNWRHGFNVGQTMFSLLVTGKLKRYFTDLEALAMVTAAFCHDIDHRGTN
NLYQMKSQNPLAKLHGSSILERHHLEFGKTLLRDESLNIFQNLNRRQHEH
AIHMMDIAIIATDLALYFKKRTMFQKIVDQSKTYETQQEWTQYMMLDQTR
KEIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLQQNP
IPMMDRNKADELPKLQVGFIDFVCTFVYKEFSRFHEEITPMLDGITNNRK
EWKALADEYETKMKGLEEEK
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 A 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)		R93 M94 S95 F113 N114 V141 F162 C163 V166 I177 V195
Binding residue
(residue number reindexed from 1)		R86 M87 S88 F106 N107 V134 F155 C156 V159 I170 V188
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: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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6mzb, PDBe:6mzb, PDBj:6mzb
PDBsum6mzb
PubMed30820458
UniProtP11541|PDE6A_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (Gene Name=PDE6A)

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