Structure of PDB 7t64 Chain D Binding Site BS01

Receptor Information

>7t64 Chain D (length=4247) Species: 9986 (Oryctolagus cuniculus)

EVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVP
PDLAICCFTLEQSLSVRALQEMLANTVHRTLLYGHAILLRHAHSRMYLSC
LTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLI
LVSVSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVL
RLFHGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWS
GSHLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSK
EKLDTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLG
VLKKKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDS
FSGKPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRS
LRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVN
LLSELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIE
SPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDL
ITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDE
VVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLH
LWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEA
FNLDGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRER
LRLEPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDPPHLERIREKLAE
NIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSG
ETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVR
LTPAQTTLVDRLAENGHNVWARDRVAQGWSYSARLVPYRLLDEATKRSNR
DSLCQAVRTLLGYGYNIEPPQSRWDRVRIFRAEKSYTVQSGRWYFEFEAV
TTGEMRVGWARPELRPDVELGADELAYVFNGHRGQRWHLGSEPFGRPWQS
GDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLG
PGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQF
EPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQNSLVEMLFLRLSLPV
QFHQLNTTTYYYSVRVFAGQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVT
VTMGDEQGNVHSSLKCSNCYMVWGGDFVSPGQQGRISHTDLVIGCLVDLA
TGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVIQFELGKQKMPL
SAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFLQVETRRAGERLG
WAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHSHTLRLYRAVCA
LGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDLLISIHLESACR
SRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRHGLPGVGVTTSLRPPH
HFSPPCFVAALPAAGVAEAPARLSPAIPLEALRDKALRMLGEAVRDGGQH
ARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEED
LEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQA
NQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDEADEEDC
PLPEDIRQDLQDFHQDLLAHCGIQLEGEEKKPQSLQELVSHMVVRWAQED
YVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECL
GQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVME
VMVNVLGGGETKEIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLE
NSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQS
CPMLLAKGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIR
KPECFGPALRGEGGSGLLAAIEEAIRISEDPARDGPRVHLGHAIMSFYAA
LIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPT
QPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASL
DTATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTV
YRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEF
AKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSL
AHKKNFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGE
NVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIEKAREG
EYNPQPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHP
LLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRGLKDMELDTSSIEK
RFAFGFLQQLLRWMDISQEFIAHLEQEIKFFAKILLPLINQYFTNHCLYF
LSTPAKVLGHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHI
LARSLDARTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRQNLTYTTVA
LLPVLTTLFQHIAQHQILDDVQVSCYRTLCSIYSLGTTKEKLRPALGECL
ARLAAAMPVAFLEPQYTTKSPRERAILGLPNSVEEMCPDIPVLDRLMADI
GGLAESGARYTEMPHVIEITLPMLCSYLPRWWERGPEAPPPALPAGAPPP
CTAVTSDHLNSLLGNILRIIVNNLGIDEATWMKRLAVFAQPIVSRARPEL
LHSHFIPTIGRLRKRAGKVVAEEEQLRLEAKAEAEEGELLVRDEFSVLCR
DLYALYPLLIRYVDNNRAHWLTEPNANAEELFRMVGEIFIYWSKSHNFKR
EEQNFVVQNEINNMSFLTARYSVQTSLIVATLKKMLPIGLNMCAPTDQDL
IMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSPSLRWQMALYRGLPGR
EEDADDPEKIVRRVQEVSAVLYHLEQTEHPTPLYNLPTHRACNMFLESYK
AAWILTEDHSFEDRMIDDLSKAGEQEEEEKKPDPLHQLVLHFSRTALTEK
SKLDEDYLYMAYADIMAKSCHLEEGGEVEVSFEEKEMEKQRLLYQQSRLH
TRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLK
DKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNG
EKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVD
YLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQG
PCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQK
DMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDI
VGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENE
MINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESIL
EYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDV
VNEGGEAEKMELFVSFCEDTIFEMQIAAQISEPEFWGELEVQRVKFLNYL
SRNFYTLRFLALFLAFAINFILLFYKVSDSPPGDENMVYYFLEESTGYME
PALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITE
QPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAEL
LGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGVIFTDNSFL
YLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMT
VGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVG
VRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAF
GELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMF
FLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

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: 7t64 Chain D Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7t64 Molecular mechanism of the severe MH/CCD mutation Y522S in skeletal ryanodine receptor (RyR1) by cryo-EM.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): C4958 C4961 H4978 H4983
• Binding residue (residue number reindexed from 1): C4168 C4171 H4188 H4193
• 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:7t64, PDBe:7t64, PDBj:7t64
• PDBsum: 7t64
• PubMed: 35867837
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)