Structure of PDB 8dvv Chain B Binding Site BS02

Receptor Information

>8dvv Chain B (length=3886) Species: 10090 (Mus musculus)

EIQFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVP
PDLSICTFVLEQSLSVRALQEMLANMKTAQGGGHRTLLYGHAILLRHSYS
GMYLCCLSTSRSSTDKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVR
VGDDLILVSVSSERYLHLSYGNSSWHVDAAFQQTLWSVAPISSGSEAAQG
YLIGGDVLRLLHGHMDECLTVPSGEHGEEQRRTVHYEGGAVSVHARSLWR
LETLRVAWSGSHIRWGQPFRLRHVTTGKYLSLMEDKNLLLMDKEKADVKS
TAFAFRSSKEKLRKEVDGMGTSEIKYGDSICYIQHVDTGLWLTYQAIQRK
AIMHHEGHMDDGLNLSRSQHEESRTARVIRSTVFLFNRFIRGLDALSKKV
IDLPIESVSLSLQDLIGYFHPPDEHLEHEDKQNRLRALKNRQNLFQEEGM
INLVLECIDRLHVYSSAAHFADVAGREAGESWKSILNSLYELLAALIRGN
RKNCAQFSGSLDWLISRLERLEASSGILEVLHCVLVESPEALNIIKEGHI
KSIISLLDKHGRNHKVLDVLCSLCVCHGVAVRSNQHLICDNLLPGRDLLL
QTRLVNHVSSMRPNIFLGVSEGSAQYKKWYYELMVDHTEPFVTAEATHLR
VGWASTEGYSPYNGVGDDLFSYGFDGLHLWSGCIARTVSSPNQHLLRTDD
VISCCLDLSAPSISFRINGQPVQGMFENFNIDGLFFPVVSFSAGIKVRFL
LGGRHGEFKFLPPPGYAACYEAVLPKEKLKVEHSREYKQERTYTRDLLGP
TLERIRERLAENIHELWVMNKIELGWQYGPVRDDNKRQHPCLVEFCKLPE
QERNYNLQMSLETLKTLLALGCHVGIADEHAEEKVKKMKLPKNYQLTSGY
KPAPMDLSFIKLTPSQEAMVDKLAENAHNVWARDRIRQGWTYGIQQDVKN
RRNPRLVPYTLLDDRTKKSNKDSLREAVRTLLGYGGERFRIFRAEKTYAV
KAGRWYFEFEAVTAGDMRVGWSRPGCQPDLELGSDDRAFAFDGFKAQRWH
QGNEHYGRSWQAGDVVGCMVDMNEHTMMFTLNGEILLDDSGSELAFKDFD
VGDGFIPVCSLGVAQVGRMNFGKDVSTLKYFTICGLQEGYEPFAVNTNRD
ITMWLSKRLPQFLQVPSNHEHIEVTRIDGTIDSSPCLKVTQKSFGSQNNN
TDIMFYRLSMPISTYYYSVRIFPGQEPANVWVGWITSDFHQYDTGFDLDR
VRTVTVTLGDEKGKVHESIKRSNCYMVCAGESMSPGQGRNNSNGLEIGCV
VDAASGLLTFIANGKELSTYYQVEPSTKLFPAVFAQATSPVLWSRMPNQF
LKVDVSRISERQGWLVQCLDPLQFMSLHIPEENRSVDILELTEQEELLQF
HYHTLRLYSAVCALGNHRVAHALCSHVDEPQLLYAIENKYMPGLLRAGYY
DLLIDIHLSSYATARLMMNNEFIVPMTEETKSITLFPDENKKHGLPGIGL
STSLRPRMRFSSPSFVSISNDCYQYSPEFPLDILKAKTIQMLTEAVKEGS
LHARDPVGGTTEFLFVPLIKLFYTLLIMGIFHNEDLKHILQLIEPGLLQM
KLPEPVKLQMCLLLQYLCDCQVRHRIEAIVAFSDDFVAKLQDNQRFRYNE
LLDFHEDLMTHCGIELDEDGSLDGSNDLTIRGRLLDLVEKVTYLKKCSSL
QQLISETMVRWAQESVIEDPELVRAMFVLLHRQYDGIGGLVRALPKTYTI
NGVSVEDTINLLASLGQIRSLLSGKEEEKLMIRGLGDIMNNKVFYQHPNL
MRALGMHETVMEVMVNVLGGGESKEITFPKMVANCCRFLCYFCRISRQNQ
KAMFDHLSYLLENSSVGLASPAMRGSTPLDVAAASVMDNNELALALREPD
LEKVVRYLAGCGLQSCQMLVSKGYPDIGWVEGERYLDFLRFAVFCNGESV
EENANVVVRLLIRRPECFGPALRGEGGNGLLAAMEEAIKIAEDPMGNAIM
TFYAALIDLLGRCAPEMHLIHAGKGEAIRIRSILRSLGDLVGVISIAFQM
PTIAKDGKVVEPDMSAGFCPDHKAAMVLFLDRVYGIEVQDFLLHLLEVGF
LPDLRAAASLSATDMALALNRYLCTAVLPLLQLRPSMMQHLLRRLVFDVP
LLNEHAKMPLKLLTNHYERCWKYYCLPGGWGNFGAASEEELHLSRKLFWG
IFDALSQKKYEQELFKLALPCLSAVAGALPPDYMESNYVSMMEKQSSMFN
PQPVDTSNITIPEKLEYFINKYAEHSHDKWSMDKLANGWIYGEIYSDSSK
IQPLMKPYKLLSEKEKEIYRWPIKESLKTMLAWGWRIERTREGDSMALYN
AAHGYSPRAIDMSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELESKGGG
NHPLLVPYDTLTAKEKAKDREKAQDIFKFLQISGYVVSRCTGGHASNKEK
EMVTSLFCKLGVLVRHLGQTLDARTVMKTGLDSVKSALRAFLDNAAEDLE
KTMENLKQGQFTHTRSQPKGVTQIINYTTVALLPMLDKHNVYSIYNTRSS
RERAALSLPANVEDVCPNIPSLEKLMTEIIELAESGIRYTQMPYMMEVVL
PMLCSYMSRWWEHGPENHPERAEMCCTALNSEHMNTLKIIYNNLGIDEGF
SQPIINKVKPQLLKTHFLPLMEKLKKKAAMVVSEEDHLKAEARGDMSEAE
LLILDEFTTLARDLYAFYPLLIRFVDYNRAKWLKEPNPYWSKSHNFKREE
QNFVVQNEINNMSFLITDTKSKMSKAAISDQERKKMKRKGDRYSMQTSLI
VAALKRLLPIGLNICAPGDQELIALAKNRFSLKDTEEEVRDIIRSNIHLQ
GKLELGIANVLFHLEQKSKYPRHRAVNLFLQGYEKSWIETEEHYFEDKLI
EDLAKPGAELPEEAMKRVDPLHQLILLFSRTALTEKCKLEEDFLYMAYAD
IMAKSCHDEEEVKSFEEKEMEKQKLLYQQARLHDRGAAEMVLQTISASKG
ETGPMVAATLKLGIAILNGGNSTVQQKMLDYLKEKKDVGFFQSLAGLMQS
CSVLDLNAFERQNKAEGLGMVTEEGSGEKVLQDDEFTCDLFRFLQLLCEG
HNSDFQNYLRTQTGNNTTVNIIISTVDYLLRVQESISDFYWYYSGKDIID
EQGQRNFSKAIQVAKQVFNTLTEYIQGPCTGNQQSLAHSRLWDAVVGFLH
VFAHMQMKLSQDSSQIELLKELMDLQKDMVVMLLSMLEGNVVNGTIGKQM
VDMLVESSNNVEMILKFFDMFLKLKDLTSSDTFKEYDPDGKGVISKRDFH
KAMESHKHYTQSETEFLLSCAETDENETLDYEEFVKRFHEPAKDIGFNVA
VLLTNLSEHMPNDTRLQTFLELAESVLNYFQPFLGRIEIMGSAKRIERVY
FEISESSRTQWEKPQVKESKRQFIFDVVNEGGEKEKMELFVNFCEDTIFE
MQLAAQIIAYQQKLLNYFARNFYNMRMLALFVAFAINFILLFYKVSVHYV
LEESSGYMEPTLRILAILHTIISFFCIIGYYCLKVPLVIFKREKEVARKL
EFDGLYITEQPSEDDIKGQWDRLVINTQSFPNNYWDKFVKRKVMDKYGEF
YGRDRISELLGMDSAVLNSIDVKYQMWKLGVVFTDNSFLYLAWYMTMSVL
GHYNNFFFAAHLLDIAMGFKTLRTILSSVTHNGKQLVLTVGLLAVVVYLY
TVVAFNFFRKFYNKSEDGDTPDMKCDDMLTCYMFHMYVGVRAGGGIGDEI
EDPAGDEYEIYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVK
EDMETKCFICGIGNDYFDTVPHGFETHTLQEHNLANYLFFLMYLINKDET
EHTGQESYVWKMYQERCWEFFPAGDCFRKQYEDQLN

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: 8dvv Chain B Residue 5002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dvv Recombinant mouse RyR2 triple phosphomimetic mutant S2807D/S2813D/S2030D in complex with FKBP12.6 and nanodisc under open-state conditions
• Resolution: 3.68 Å
• Binding residue (original residue number in PDB): C4890 H4907 H4912
• Binding residue (residue number reindexed from 1): C3810 H3827 H3832
• 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:8dvv, PDBe:8dvv, PDBj:8dvv
• PDBsum: 8dvv
• UniProt: E9Q401|RYR2_MOUSE Ryanodine receptor 2 (Gene Name=Ryr2)