Structure of PDB 8dve Chain D Binding Site BS03

Receptor Information
>8dve Chain D (length=3942) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPP
DLAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLT
TSRKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSS
ERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGE
CLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQP
LRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEEGMGPPEI
KYGESLCFVQHVASGLWLTYAALKKKAILHQEGHMDDALFLTRCQQEESQ
AARMIHSTAGLYNQFIKGLDSFSGKPRPALPIEAVILSLQDLIGYFEPPS
EELQHEEKQSKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEY
AGEEAAESWKEIVNLLYELLASLIRGNRANCALFSTNLDWVVSKLDRLEA
SSGILEVLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSL
CVCNGVAVRSNQDLITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGS
TQYGKWYFEVMVDEVVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNG
VGDDLYSYGFDGLHLWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSIS
FRINGCPVQGVFEAFNLDGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPP
GYAPCHEAVLPRERLRLEPIKEYRREGPRGPHLVGPSRCLSHTDFVPIVL
PPHLERIREKLAENIHELWALTRILPEPERNYNLQMSGETLKTLLALPAQ
TTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRLLDEAT
KRSNRDSLCQAVRTLLGYGYNIEPDRVRIFRAEKSYTVQSGRWYFEFEAV
TTGEMRVGWARPELRPDVELGADELAYVFNGHRGQRWHLGSEPFGRPWQS
GDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLG
PGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQF
EPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQNSLVEMLFLRLSLPV
QFHQHFRDDPEIILNTTTYYYSVRVFAGQEPSCVWVGWVTPDYHQHDMNF
DLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVHTDLVIGCLVDLA
TGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVIQFELGKQKNIM
PLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFLQVETRRAGER
LGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHSHTLRLYRAV
CALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDLLISIHLESA
CRSRRSMLSEYIVPLTPETRAITLFPPRHGLPGVGVTTSLRPPHHFSPPC
FVAALPAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQ
FVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEEEGLLQMKLPESVK
LQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTM
SAAETARRTREFRSPPQEQINMLLHFKDDCPLPEDIRQDLQDFHQDLLAH
CGIQPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLR
ALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIM
NNKVFYQHPNLMRALGMHETVMEVMVNVLGEIRFPKMVTSCCRFLCYFCR
ISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALALQ
EQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVFV
NGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDPA
RDNRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLV
PLDDLVGIISLPLQIPVQPKMSASFVPDHKASMVLFLDRVYGIENQDFLL
HVLDVGFLPDMRAAASLDTATFSTTEMALALNRYLCLAVLPLITKCAPLF
AGTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSML
QHLLRRLVFDVPILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSE
EELHLTRKLFWGIFDSLAHKKYDQELYRMAMPCLCAIAPEKLDSFINKFA
EYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPI
KESLKAMIAWEWTIEKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQP
PDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYD
TLTAKEKARDREKAQELLKFLQMNGYAVTRIEKRFAFGFLQQLLRWMDIS
QEFIAHLEAHEQEIKFFAKILLPLINQYFTNHCLYFLSNKEKEMITSLFC
KLAALVRHVVNCLHILARKAGLRSFFESASEDIEKMVENLRQNLTYTTVA
LLPVLTTLFQHIAQHDVQVSCYRTLCSIYSLRPALGECLARLAARLMADI
GGLAPHVIEITLPMLCSYLPRWSDHLNSLLGNILRIIVNNRLAVFAQPIV
SRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRDEFSVLCRDLYALYPL
LIRYVDNNRAHWLTEPNANAEELFRMVGEIFIYWSKSHNFKREEQNFVVQ
NEIVATLKKMLPIGLNMCDQDLIMLAKTRYALKDTDEEVREFLQNDPEKI
VRRVQEVSAVLYHLEQTEHSKQRRRAVVACFRMTPLYNLPTHRACNMFLE
SYKAAWILTEDHSFEDRMIDDLSKAGKKPDPLHQLVLHFSRTALTEKSKL
DEDYLYMAYADIMAKSCHLEEVSFEEKEMEKQRLLYQQSRLHTRGAAEMV
LQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFF
QSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDE
FTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQES
ISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQS
LAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLS
LLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQD
YVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINFEEFA
NRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLG
RIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAE
KMELFVSFCEDTIFEMQIAAQISETAREAATALAALLWAVVARWGELEVQ
RVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPNMVYYFLEES
TGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDG
LYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRE
RIAELLGMDLASLEITAHNERTWLMSIDVKYQIWKFGVIFTDNSFLYLGW
YMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLL
AVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAG
GGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELR
DQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMY
LINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8dve Chain D Residue 5103 [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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PDB8dve Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation.
Resolution3.84 Å
Binding residue
(original residue number in PDB)		R4215 M4954 C4958 F4975 T4979 L4985
Binding residue
(residue number reindexed from 1)		R3436 M3860 C3864 F3881 T3885 L3891
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005216 monoatomic ion channel activity
GO:0005219 ryanodine-sensitive calcium-release channel activity
GO:0005245 voltage-gated calcium channel activity
GO:0005262 calcium channel activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005524 ATP binding
GO:0015278 intracellularly gated calcium channel activity
GO:0015643 toxic substance binding
GO:0035381 ATP-gated ion channel activity
GO:0042802 identical protein binding
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
GO:0097718 disordered domain specific binding
Biological Process
GO:0003151 outflow tract morphogenesis
GO:0006811 monoatomic ion transport
GO:0006816 calcium ion transport
GO:0006874 intracellular calcium ion homeostasis
GO:0006936 muscle contraction
GO:0006941 striated muscle contraction
GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0019722 calcium-mediated signaling
GO:0043588 skin development
GO:0043931 ossification involved in bone maturation
GO:0048741 skeletal muscle fiber development
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051289 protein homotetramerization
GO:0055085 transmembrane transport
GO:0070588 calcium ion transmembrane transport
GO:0071277 cellular response to calcium ion
GO:0071313 cellular response to caffeine
Cellular Component
GO:0005790 smooth endoplasmic reticulum
GO:0014802 terminal cisterna
GO:0016020 membrane
GO:0016529 sarcoplasmic reticulum
GO:0030018 Z disc
GO:0031090 organelle membrane
GO:0033017 sarcoplasmic reticulum membrane
GO:0034704 calcium channel complex
GO:0042383 sarcolemma
GO:1990425 ryanodine receptor complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dve, PDBe:8dve, PDBj:8dve
PDBsum8dve
PubMed37224245
UniProtP11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)

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