Structure of PDB 7vmm Chain D Binding Site BS01

Receptor Information

>7vmm Chain D (length=4044) Species: 10090 (Mus musculus)

IQFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVPP
DLSICTFVLEQSLSVRALQEMLANGHRTLLYGHAILLRHSYSGMYLCCLS
TSRSSTDKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILV
SVSSERYLHLSYGNSSWHVDAAFQQTLWSVAPISSGSEAAQGYLIGGDVL
RLLHGHMDECLTVPSGEHGEEQRRTVHYEGGAVSVHARSLWRLETLRVAW
SGSHIRWGQPFRLRHVTTGKYLSLMEDKNLLLMDKEKADVKSTAFAFRSS
KEKLDVGVRKEVDGMGTSEIKYGDSICYIQHVDTGLWLTYQAVDVKSARM
GSIQRKAIMHHEGHMDDGLNLSRSQHEESRTARVIRSTVFLFNRFIRGLD
ALSKKVKLPTIDLPIESVSLSLQDLIGYFHPPDEHLEHEDKQNRLRALKN
RQNLFQEEGMINLVLECIDRLHVYSSAAHFADVAGREAGESWKSILNSLY
ELLAALIRGNRKNCAQFSGSLDWLISRLERLEASSGILEVLHCVLVESPE
ALNIIKEGHIKSIISLLDKHGRNHKVLDVLCSLCVCHGVAVRSNQHLICD
NLLPGRDLLLQTRLVNHVSSMRPNIFLGVSEGSAQYKKWYYELMVDHTEP
FVTAEATHLRVGWASTEGYSPYPGGGEEWGGNGVGDDLFSYGFDGLHLWS
GCIARTVSSPNQHLLRTDDVISCCLDLSAPSISFRINGQPVQGMFENFNI
DGLFFPVVSFSAGIKVRFLLGGRHGEFKFLPPPGYAACYEAVLPKEKLKV
EHSREYKQERTYTRDLLGPTVSLTQAVPVDTSQIVLPPHLERIRERLAEN
IHELWVMNKIELGWQYGPVRDDNKRQHPCLVEFCKLPEQERNYNLQMSLE
TLKTLLALGCHVGIAYQLTSGYKPAPMDLSFIKLTPSQEAMVDKLAENAH
NVWARDRIRQRRNPRLVPYTLLDDRTKKSNKDSLREAVRTLLGYGYRFRI
FRAEKTYAVKAGRWYFEFEAVTAGDMRVGWSRPGCQPDLELGSDDRAFAF
DGFKAQRWHQGNEHYGRSWQAGDVVGCMVDMNEHTMMFTLNGEILLDDSG
SELAFKDFDVGDGFIPVCSLGVAQVGRMNFGKDVSTLKYFTICGLQEGYE
PFAVNTNRDITMWLSKRLPQFLQVPSNHEHIEVTRIDKVTQKSFGSQNNN
TDIMFYRLSMPIECAAAAAAAAAAAAAAAAAAAAAAAAAAAAADSDFEVL
MKTAHGHLVPDRIDKDKETPKPEFNNHKDYAQEKPSRLKQAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
PLSAGLFKSEHKNPVPQCPPRLHVQFLSHVLWSRMPNQFLKVDVSRISER
QGWLVQCLDPLQFMSLHIPEENRSVDILELTEQEELLQFHYHTLRLYSAV
CALGNHRVAHALCSHVDEPQLLYAIENKYMPGLLRAGYYDLLIDIHLSSY
ATARLMMNNEFIVPMTEETKSITLFPDENKKHGLPGIGLSTSLRPRMRFS
SPSFVSISNDCYQYSPEFPLDILKAKTIQMLTEAVKEGSLHARDPVGGTT
EFLFVPLIKLFYTLLIMGIFHNEDLKHILQLIEPSGLLQMKLPEPVKLQM
CLLLQYLCDCQVRHRIEAIVAFSDDFVAKLQDNQRFRYNEVMQALNMSAA
LTARKTREFRSPPQEQINMLLNFKDDKSECPCPEEIRDQLLDFHEDLMTH
CGIESLQQLISETMVRWAQESVIEDPELVRAMFVLLHRQYDGIGGLVRAL
PKTYTINGVSVEDTINLLASLGQIRSLLSVRMGKEEEKLMIRGLGDIMNN
KVFYQHPNLMRALGMHETVMEVMVNVLGGGESKEITFPKMVANCCRFLCY
FCRISRQNQKAMFDHLSYLLENSSVGLASPAMRGSTPLDVAAASVMDNNE
LALALREPDLEKVVRYLAGCGLQSCQMLVSKGYPDIGWNPVEGERYLDFL
RFAVFCNGESVEENANVVVRLLIRRPECFGPALRGEGGNGLLAAMEEAIK
IAEDPSRDGPDTIHMGNAIMTFYAALIDLLGRCAPEMHLIHAGKGEAIRI
RSILRSLIPLGDLVGVISIAFQMPEPDMSAGFCPDHKAAMVLFLDRVYGI
EVQDFLLHLLEVGFLPDLRAAASLDTAALSAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIPEKLEYFINKYAEHSHDK
WSMDKLANGWIYGEIYSDSSKIQPLMLLSEKEKEIYRWPIKESLKTMLAW
DLHAMAEMMAENYHNIWAKKKKLELESKGGGNHPLLVPYDTLTAKEKAKD
REKAQDIFKFLQISGYVVSRGAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAPRHRAVNLFLQGYEKSWIE
TEEHYFEDKLIEDLAKPGARVDPLHQLILLFSRTALTEKCKLEEDFLYMA
YADIMAKSCHSFEEKEMEKQKLLYQQARLHDRGAAEMVLQTISASKGETG
PMVAATLKLGIAILNGGNSTVQQKMLDYLKEKKDVGFFQSLAGLMQSCSV
LDLNAFERQNKAEGLGMVTEEGSGEKVLQDDEFTCDLFRFLQLLCEGHNS
DFQNYLRTQTGNNTTVNIIISTVDYLLRVQESISDFYWYYSGKDIIDEQG
QRNFSKAIQVAKQVFNTLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFA
HMQMKLSQDSSQIELLKELMDLQKDMVVMLLSMLEGNVVNGTIGKQMVDM
LVESSNNVEMILKFFDMFLKLKDLTSSDTFKEYDPDGKGVISKRDFHKAM
ESHKHYTQSETEFLLSCAETDENETLDYEEFVKRFHEPAKDIGFNVAVLL
TNLSEHMPNDTRLQTFLELAESVLNYFQPFLGRIEIMGSAKRIERVYFEI
SESSRTQWEKPQVKESKRQFIFDVVNEGGEKEKMELFVNFCEDTIFEMQL
AAQIMTVKDMVLAFFSSYWSVFVTLLHFVASVCRGFFRIVSSLFWKKIIA
YQQKLLNYFARNFYNMRMLALFVAFAINFILLFYKVSVHYVLEESSGYME
PTLRILAILHTIISFFCIIGYYCLKVPLVIFKREKEVARKLEFDGLYITE
QPSEDDIKGQWDRLVINTQSFPNNYWDKFVKRKVMDKYGEFYGRDRISEL
LGMDKAALDFSDAREKKKPKKDSSLSAVLNSIDVKYQMWKLGVVFTDNSF
LYLAWYMTMSVLGHYNNFFFAAHLLDIAMGFKTLRTILSSVTHNGKQLVL
TVGLLAVVVYLYTVVAFNFFRKFYNKSEDGDTPDMKCDDMLTCYMFHMYV
GVRAGGGIGDEIEDPAGDEYEIYRIIFDITFFFFVIVILLAIIQGLIIDA
FGELRDQQEQVKEDMETKCFICGIGNDYFDTVPHGFETHTLQEHNLANYL
FFLMYLINKDETEHTGQESYVWKMYQERCWEFFPAGDCFRKQYE

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: 7vmm Chain D Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7vmm Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): C4887 H4907 H4912
• Binding residue (residue number reindexed from 1): C3969 H3989 H3994
• 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:7vmm, PDBe:7vmm, PDBj:7vmm
• PDBsum: 7vmm
• PubMed: 35595836
• UniProt: E9Q401|RYR2_MOUSE Ryanodine receptor 2 (Gene Name=Ryr2)