Structure of PDB 8dty Chain B Binding Site BS01

Receptor Information

>8dty Chain B (length=4004) Species: 10090 (Mus musculus)

EIQFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVP
PDLSICTFVLEQSLSVRALQEMLGGGHRTLLYGHAILLRHSYSGMYLCCL
STSRSSTDKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLIL
VSVSSERYLHLSYGNSSWHVDAAFQQTLWSVAPISSGSEAAQGYLIGGDV
LRLLHGHMDECLTVPSGEHGEEQRRTVHYEGGAVSVHARSLWRLETLRVA
WSGSHIRWGQPFRLRHVTTGKYLSLMEDKNLLLMDKEKADVKSTAFAFRS
SKEKLRKEVDGMGTSEIKYGDSICYIQHVDTGLWLTYQAVDIQRKAIMHH
EGHMDDGLNLSRSQHEESRTARVIRSTVFLFNRFIRGLDALSKKVKLPTI
DLPIESVSLSLQDLIGYFHPPDEHLEHEDKQNRLRALKNRQNLFQEEGMI
NLVLECIDRLHVYSSAAHFADVAGREAGESWKSILNSLYELLAALIRGNR
KNCAQFSGSLDWLISRLERLEASSGILEVLHCVLVESPEALNIIKEGHIK
SIISLLDKHGRNHKVLDVLCSLCVCHGVAVRSNQHLICDNLLPGRDLLLQ
TRLVNHVSSMRPNIFLGVSEGSAQYKKWYYELMVDHTEPFVTAEATHLRV
GWASTEGYSPYPGGGEEWGGNGVGDDLFSYGFDGLHLWSGCIARTVSSPN
QHLLRTDDVISCCLDLSAPSISFRINGQPVQGMFENFNIDGLFFPVVSFS
AGIKVRFLLGGRHGEFKFLPPPGYAACYEAVLPKEKLKVEHSREYKQERT
YTRDLLGPTVSLTQAAFTPVPVDTSQIVLPPHLERIRERLAENIHELWVM
NKIELGWQYGPVRDDNKRQHPCLVEFCKLPEQERNYNLQMSLETLKTLLA
LGCHVGIADEHAEEKVKKMKLPKNYQLTSGYKPAPMDLSFIKLTPSQEAM
VDKLAENAHNVWARDRIRQGWTYGIQQDVKNRRNPRLVPYTLLDDRTKKS
NKDSLREAVRTLLGYGYHLEAPDQDHASRAEVCSGTGERFRIFRAEKTYA
VKAGRWYFEFEAVTAGDMRVGWSRPGDLELGSDDRAFAFDGFKAQRWHQG
NEHYGRSWQAGDVVGCMVDMNEHTMMFTLNGEILLDDSGSELAFKDFDVG
DGFIPVCSLGVAQVGRMNFGKDVSTLKYFTICGLQEGYEPFAVNTNRDIT
MWLSKRLPQFLQVPSNHEHIEVTRIDGTIDSSPCLKVTQKSFGSQNNNTD
IMFYRLSMPIEYLMQTSTYYYSVRIFPGQEPANVWVGWITSDFHQYDTGF
DLDRVRTVTVTLGDEKGKVHESIKRSNCYMVCAGESMSPGQGRNNSNGLE
IGCVVDAASGLLTFIANGKELSTYYQVEPSTKLFPAVFAQATSPNVFQFE
VLWSRMPNQFLKVDVSRISERQGWLVQCLDPLQFMSLHIPEENRSVDILE
LTEQEELLQFHYHTLRLYSAVCALGNHRVAHALCSHVDEPQLLYAIENKY
MPGLLRAGYYDLLIDIHLSSYATARLMMNNEFIVPMTEETKSITLFPDEN
KKHGLPGIGLSTSLRPRMRFSSPSFVSISNDCYQYSPEFPLDILKAKTIQ
MLTEAVKEGSLHARDPVGGTTEFLFVPLIKLFYTLLIMGIFHNEDLKHIL
QLIEPGLLQMKLPEPVKLQMCLLLQYLCDCQVRHRIEAIVAFSDDFVAKL
QDNQRFRYNEVMQALNMSAALTARKCPEEIRDQLLDFHEDLMTHCGIELD
EDGSLDGSNDLTIRGRLLDLVEKVTYLKKSSLQQLISETMVRWAQESVIE
DPELVRAMFVLLHRQYDGIGGLVRALPKTYTINGVSVEDTINLLASLGQI
RSLLSVRMGKEEEKLMIRGLGDIMNNKVFYQHPNLMRALGMHETVMEVMV
NVLGGGESKEITFPKMVANCCRFLCYFCRISRQNQKAMFDHLSYLLENSS
VGLASPAMRGSTPLDVAAASVMDNNELALALREPDLEKVVRYLAGCGLQS
CQMLVSKGYPDIGWNPVEGERYLDFLRFAVFCNGESVEENANVVVRLLIR
RPECFGPALRGEGGNGLLAAMEEAIKIAEDPSRDGPSPTMGNAIMTFYAA
LIDLLGRCAPEMHLIHAGKGEAIRIRSILRSLGDLVGVISIAFQMPTIAK
DGKVVEPDMSAGFCPDHKAAMVLFLDRVYGIEVQDFLLHLLEVGFLPDLR
AAASLDTAALSATDMALALNRYLCTAVLPLLCGQLRPSMMQHLLRRLVFD
VPLLNEHAKMPLKLLTNHYERCWKYYCLPGGWGNFGAASEEELHLSRKLF
WGIFDALSQKKYEQELFKLALPCLSAVAGALPPDYMESNYVSMMEKQSSM
FNPQPVDTSNITIPEKLEYFINKYAEHSHDKWSMDKLANGWIYGEIYSDS
SKIQPLMKPYKLLSEKEKEIYRWPIKESLKTMLAWGWRIERTREGDSMAL
YNAAHGYSPRAIDMSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELESKG
GGNHPLLVPYDTLTAKEKAKDREKAQDIFKFLQISGYVVSRLSAASRPLC
TGGHASNKEKEMVTSLFCKLGVLVRHLGQTLDARTVMKTGLDSVKSALRA
FLDNAAEDLEKTMENLKQGQFTHTRSQPKGVTQIINYTTVALLPMLDKHN
VYSIYNTRSSRERAALSLPANVEDVCPNIPSLEKLMTEIIELAESGIRYT
QMPYMMEVVLPMLCSYMSRWWEHGPENHPERAEMCCTALNSEHMNTLKII
YNNLGIDEGFSQPIINKVKPQLLKTHFLPLMEKLKKKAAMVVSEEDHLKA
EARGDMSEAELLILDEFTTLARDLYAFYPLLIRFVDYNRAKWLKEPNPYW
SKSHNFKREEQNFVVQNEINNMSFLITDTKSKMSKAAISDQERKKMKRKG
DRYSMQTSLIVAALKRLLPIGLNICAPGDQELIALAKNRFSLKDTEEEVR
DIIRSNIHLQGKLELGIANVLFHLEQKSKYPRHRAVNLFLQGYEKSWIET
EEHYFEDKLIEDLAKPGAELPEEDEAMKRVDPLHQLILLFSRTALTEKCK
LEEDFLYMAYADIMAKSCHDEEDDDGEEEVKSFEEKEMEKQKLLYQQARL
HDRGAAEMVLQTISASKGETGPMVAATLKLGIAILNGGNSTVQQKMLDYL
KEKKDVGFFQSLAGLMQSCSVLDLNAFERQNKAEGLGMVTEEGSGEKVLQ
DDEFTCDLFRFLQLLCEGHNSDFQNYLRTQTGNNTTVNIIISTVDYLLRV
QESISDFYWYYSGKDIIDEQGQRNFSKAIQVAKQVFNTLTEYIQGPCTGN
QQSLAHSRLWDAVVGFLHVFAHMQMKLSQDSSQIELLKELMDLQKDMVVM
LLSMLEGNVVNGTIGKQMVDMLVESSNNVEMILKFFDMFLKLKDLTSSDT
FKEYDPDGKGVISKRDFHKAMESHKHYTQSETEFLLSCAETDENETLDYE
EFVKRFHEPAKDIGFNVAVLLTNLSEHMPNDTRLQTFLELAESVLNYFQP
FLGRIEIMGSAKRIERVYFEISESSRTQWEKPQVKESKRQFIFDVVNEGG
EKEKMELFVNFCEDTIFEMQLAAQIIAYQQKLLNYFARNFYNMRMLALFV
AFAINFILLFYKVSVHYVLEESSGYMEPTLRILAILHTIISFFCIIGYYC
LKVPLVIFKREKEVARKLEFDGLYITEQPSEDDIKGQWDRLVINTQSFPN
NYWDKFVKRKVMDKYGEFYGRDRISELLGMDSAVLNSIDVKYQMWKLGVV
FTDNSFLYLAWYMTMSVLGHYNNFFFAAHLLDIAMGFKTLRTILSSVTHN
GKQLVLTVGLLAVVVYLYTVVAFNFFRKFYNKSEDGDTPDMKCDDMLTCY
MFHMYVGVRAGGGIGDEIEDPAGDEYEIYRIIFDITFFFFVIVILLAIIQ
GLIIDAFGELRDQQEQVKEDMETKCFICGIGNDYFDTVPHGFETHTLQEH
NLANYLFFLMYLINKDETEHTGQESYVWKMYQERCWEFFPAGDCFRKQYE
DQLN

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: 8dty Chain B Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dty Recombinant mouse RyR2 triple phosphomimetic mutant S2807D/S2813D/S2030D in complex with FKBP12.6 and nanodisc under closed-state conditions
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): H4907 H4912
• Binding residue (residue number reindexed from 1): H3945 H3950
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0005219 ryanodine-sensitive calcium-release channel activity
• GO:0005262 calcium channel activity
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005516 calmodulin binding
• GO:0015278 intracellularly gated calcium channel activity
• GO:0019899 enzyme binding
• GO:0019901 protein kinase binding
• GO:0034236 protein kinase A catalytic subunit binding
• GO:0034237 protein kinase A regulatory subunit binding
• GO:0042802 identical protein binding
• GO:0043924 suramin binding
• GO:0048763 calcium-induced calcium release activity
• GO:0097159 organic cyclic compound binding

Biological Process

• GO:0001666 response to hypoxia
• GO:0002027 regulation of heart rate
• GO:0003143 embryonic heart tube morphogenesis
• GO:0003220 left ventricular cardiac muscle tissue morphogenesis
• GO:0003300 cardiac muscle hypertrophy
• GO:0005513 detection of calcium ion
• GO:0006811 monoatomic ion transport
• GO:0006816 calcium ion transport
• GO:0006874 intracellular calcium ion homeostasis
• GO:0010460 positive regulation of heart rate
• GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
• GO:0010882 regulation of cardiac muscle contraction by calcium ion signaling
• GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
• GO:0014850 response to muscle activity
• GO:0019722 calcium-mediated signaling
• GO:0031000 response to caffeine
• GO:0035994 response to muscle stretch
• GO:0051209 release of sequestered calcium ion into cytosol
• GO:0051284 positive regulation of sequestering of calcium ion
• GO:0051649 establishment of localization in cell
• GO:0051775 response to redox state
• GO:0055085 transmembrane transport
• GO:0055117 regulation of cardiac muscle contraction
• GO:0060048 cardiac muscle contraction
• GO:0060402 calcium ion transport into cytosol
• GO:0070588 calcium ion transmembrane transport
• GO:0071313 cellular response to caffeine
• GO:0071872 cellular response to epinephrine stimulus
• GO:0072599 establishment of protein localization to endoplasmic reticulum
• GO:0086005 ventricular cardiac muscle cell action potential
• GO:0086029 Purkinje myocyte to ventricular cardiac muscle cell signaling
• GO:0097050 type B pancreatic cell apoptotic process
• GO:0097553 calcium ion transmembrane import into cytosol
• GO:0098735 positive regulation of the force of heart contraction
• GO:0098904 regulation of AV node cell action potential
• GO:0098907 regulation of SA node cell action potential
• GO:0098910 regulation of atrial cardiac muscle cell action potential
• GO:0098911 regulation of ventricular cardiac muscle cell action potential

Cellular Component

• GO:0005790 smooth endoplasmic reticulum
• GO:0016020 membrane
• GO:0016529 sarcoplasmic reticulum
• GO:0030017 sarcomere
• GO:0030018 Z disc
• GO:0032991 protein-containing complex
• GO:0033017 sarcoplasmic reticulum membrane
• GO:0034704 calcium channel complex

External links

• PDB: RCSB:8dty, PDBe:8dty, PDBj:8dty
• PDBsum: 8dty
• UniProt: E9Q401|RYR2_MOUSE Ryanodine receptor 2 (Gene Name=Ryr2)