Structure of PDB 8duj Chain G Binding Site BS04

Receptor Information

>8duj Chain G (length=3933) Species: 9986 (Oryctolagus cuniculus)

VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPP
DLAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLT
TSRKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSS
ERYLHLSTLQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGECLTI
SAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIR
HVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEMGPPEIKYGESL
CFVQHVASGLWLTYAALKKKAILHQEGHMDDALFLTRCQQEESQAARMIH
STAGLYNQFIKGLDSFSGKPRLPIEAVILSLQDLIGYFEPPQSKLRSLRN
RQSLFQEEGMLSLVLNCIDRLNVYTTEEAAESWKEIVNLLYELLASLIRG
NRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPEVLNIIQENH
IKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLLPGRELL
LQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFLTAQATHL
RVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGHVARPVTS
PGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDGLFFPVVS
FSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRLEPIKEYRRE
GPPHLVGPSRCLSHTDFVPIVLPPHLERIREKLAENIHELWALTRIHPCL
VNFHSLPEPERNYNLQMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPK
TYMMSNGYKPAPLDLSHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSY
SAVQDIPARRNPRLVPYRLLDEATKRSNRDSLCQAVRTLLGYGYNIEPDR
VRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELA
YVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMS
DSGSETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQE
GFEPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLR
LAHRTWGSQNSLVEMLFLRLSLPVQFHQHFRILNTTTYYYSVRVFAGQEP
SCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMHSSLKCSNCYMVWGGDFVH
TDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNV
IQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNH
FLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQR
FHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGY
YDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPRHGLPGVGVTTS
LRPPHHFSPPCFVAALPPARLSPAIPLEALRDKALRMLGEAVRDGGQHAR
DPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEEEGL
LQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSR
YALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDDCPLPEDIRQDL
QDFHQDLLAHCGIQLPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLH
RQYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEE
NLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGEIRFPKMVT
SCCRFLCYFCRISRQNQRSMFDHLSYLLENSMQGSTPLDVAAASVIDNNE
LALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFL
RFAVFVNGESVEENANVVVRLLIRKPECFGPALRGSGLLAAIEEAIRISE
DPNRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLV
PLDDLVGIISLPLQIPVQPKMSASFVPDHKASMVLFLDRVYGIENQDFLL
HVLDVGFLPDMRAAASLDTEMALALNRYLCLAVLPLITKCAPLFAGTEHR
AIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRR
LVFDVPILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLT
RKLFWGIFDSLAHKKYDQELYRMAMPCLCAIAPEKLDSFINKFAEYTHEK
WAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKA
MIAWEWTIEKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGV
TLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKE
KARDREKAQELLKFLQMNGYAVTRIEKRFAFGFLQQLLRWMDISQEFIAH
LEAHEQEIKFFAKILLPLINQYFTNHCLYFLSNKEKEMITSLFCKLAALV
RHVVNCLHILARKAGLRSFFESASEDIEKMVENLRQNLTYTTVALLPVLT
TLFQHIAQHDVQVSCYRTLCSIYSLRPALGECLARLAARLMADIGGLAPH
VIEITLPMLCSYLPRWSDHLNSLLGNILRIIVNNRLAVFAQPIVSRARPE
LLHSHFIPTIGRLRKRAGKVVAEEEQLRDEFSVLCRDLYALYPLLIRYVD
NNRAHWLTEPNANAEELFRMVGEIFIYWSKSHNFKREEQNFVVQNEIVAT
LKKMLPIGLNMCDQDLIMLAKTRYALKDTDEEVREFLQNDPEKIVRRVQE
VSAVLYHLEQTEHSKQRRRAVVACFRMTPLYNLPTHRACNMFLESYKAAW
ILTEDHSFEDRMIDDLSKAGKKPDPLHQLVLHFSRTALTEKSKLDEDYLY
MAYADIMAKSCHLEEVSFEEKEMEKQRLLYQQSRLHTRGAAEMVLQMISA
CKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQAL
MQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLF
RFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQESISDFYW
YYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRL
WDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNV
VNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQDYVTDPR
GLISKKDFQKAMDSQKQFTGPEIQFLLSCSEEMINFEEFANRFQEPARDI
GFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLGRIEIMGASRR
IERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAEKMELFVSFCE
DTIFEMQIAAQISETAREAATALAALLWAVVARWGELEVQRVKFLNYLSR
NFYTLRFLALFLAFAINFILLFYKVSDSPPNMVYYFLEESTGYMEPALWC
LSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPGDD
DVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGMDL
ASLEITAHNERTWLMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHY
NNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVV
AFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDP
AGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDM
ETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHT
GQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

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 G 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): H4978 H4983
• Binding residue (residue number reindexed from 1): H3874 H3879
• 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)