Structure of PDB 8duj Chain J Binding Site BS04

Receptor Information

>8duj Chain J (length=3892) Species: 9986 (Oryctolagus cuniculus)

QFLRTDDEVVLQCSAQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICC
FTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMT
DKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSER
YLHLSTASGELQVDASFMQTLWNMNPIYVTGGHVLRLFHECLTISARRLV
YYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVTTGRYLVVVD
ACKAHTKATSFCFRVSCFVQHVASGLWLTYALKKKAILHQEGHMDDALFL
TRCQQEESQAARMIHSTAGLYNQFIKGLDSFSGKPRALPIEAVILSLQDL
IGYFEPPSEELQHEEKQSKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYT
TAAHFAEYAGEEAAESWKEIVNLLYELLASLIRGNRANCALFSTNLDWVV
SKLDRLEASSGILEVLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHK
VLDVLCSLCVCNGVAVRSNQDLITENLLPGRELLLQTNLINYVTSIRPNI
FVGRAEGSTQYGKWYFEVMVDEVVPFLTAQATHLRVGWALTEGYSPYPGG
GEGWGGNGVGDDLYSYGFDGLHLWTGHVARPVTSPGQHLLAPEDVVSCCL
DLSVPSISFRINGCPVQGVFEAFNLDGLFFPVVSFSAGVKVRFLLGGRHG
EFKFLPPPGYAPCHEAVLPRERLRLEPIKEYRREGPPHLVGPSRCLSHTD
FVPPHLERIREKLAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFH
SLPEPERNYNLQMSGETLKTLLALGAQTTLVDRLAENGHNVWARDRVAQG
WSYSAVQDIPARRNPRLVPYRLLDEATKRSNRDSLCQAVRTLLGYGDRVR
IFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYV
FNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDS
GSETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGF
EPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLA
HRTWGSQNSLVEMLFLRLSLPVQFHQHFRCLNTTTYYYSVRVFAGQEPSC
VWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWG
GDFVHTDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLP
THQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWS
RMPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSER
LDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGP
LRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPRHGLPGV
GVTTSLRPPHHFSPPCFVAALPPARLSPAIPLEALRDKALRMLGEAVRDG
GQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFT
EEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQA
NQRSRYALLMRAAETARRTREFRSPPQEQINMLLHFKDDCPLPEDIRQDL
QDFHQDLLAHCGIQPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHR
QYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEEN
LMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGEIRFPKMVTS
CCRFLCYFCRISRQNQRSMFDHLSYLLENSMQGSTPLDVAAASVIDNNEL
ALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLR
FAVFVNGESVEENANVVVRLLIRKPECFGPALRGSGLLAAIEEAIRISED
PARDGPNRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAIL
RSLVPLDDLVGIISLPLQIPTVQPKMSASFVPDHKASMVLFLDRVYGIEN
QDFLLHVLDVGFLPDMRAAASLDTEMALALNRYLCLAVLPLITKCAPLFA
GTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQ
HLLRRLVFDVPILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEE
ELHLTRKLFWGIFDSLAHKKYDQELYRMAMPCLCAIAGALPPEKLDSFIN
KFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYR
WPIKESLKAMIAWEWTIEKAREGEEERTEKKKTRKISQTAQTYDPREGYN
PQPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLV
PYDTLTAKEKARDREKAQELLKFLQMNGYAVTRIEKRFAFGFLQQLLRWM
DISQEFIAHLEAHEQEIKFFAKILLPLINQYFTNHCLYFLSNKEKEMITS
LFCKLAALVRHVVNCLHILARKAGLRSFFESASEDIEKMVENLRQNLTYT
TVALLPVLTTLFQHIAQHDVQVSCYRTLCSIYSLRPALGECLARLAARLM
ADIGGLAPHVIEITLPMLCSYLPRWSDHLNSLLGNILRIIVNNRLAVFAQ
PIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQRDEFSVLCRDLYALY
PLLIRYVDNNRAHWLTEPNANAEELFRMVGEIFIYWSKSHNFKREEQNFV
VQNEIVATLKKMLPIGLNMCAPTDQDLIMLAKTRYALKDTDEEVREFLQN
DPEKIVRRVQEVSAVLYHLEQTEHSKQRRRAVVACFRMTPLYNLPTHRAC
NMFLESYKAAWILTEDHSFEDRMIDDLSKAGEKKPDPLHQLVLHFSRTAL
TEKSKLDEDYLYMAYADIMAKSCHLEVSFEEKEMEKQRLLYQQSRLHTRG
AAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKK
EVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKV
MADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLL
RLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCT
GNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMV
VMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGS
EAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEINFEEFAN
RFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLGR
IEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAEK
MELFVSFCEDTIFEMQIAAQISETAREAATALAALLWAVVARAGAWGELE
VQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPNMVYYFLE
ESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEF
DGLYITEQPDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRER
IAELLGMDLASLEITAHNERTWLMSIDVKYQIWKFGVIFTDNSFLYLGWY
MVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLA
VVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGG
GIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRD
QQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYL
INKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 8duj Chain J Residue 5104

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8duj Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): C4958 C4961 H4978 H4983
• Binding residue (residue number reindexed from 1): C3813 C3816 H3833 H3838
• Annotation score: 1

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

External links

• PDB: RCSB:8duj, PDBe:8duj, PDBj:8duj
• PDBsum: 8duj
• PubMed: 37224245
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)