Structure of PDB 7t65 Chain D Binding Site BS01

Receptor Information

>7t65 Chain D (length=4252) Species: 9986 (Oryctolagus cuniculus)

EVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVP
PDLAICCFTLEQSLSVRALQEMLANTVEGGGHRTLLYGHAILLRHAHSRM
YLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVG
DDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTG
GHVLRLFHGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLR
ISWSGSHLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCF
RVSKEKLDTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKA
LRLGVLKKKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIK
GLDSFSGKPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQS
KLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWK
EIVNLLSELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYC
VLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRS
NQDLITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEV
MVDEVVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGF
DGLHLWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQG
VFEAFNLDGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVL
PRERLRLEPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDIVLPPHLER
IREKLAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERN
YNLQMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAP
LDLSHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSARLVPYRLLDE
ATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPNQSRWDRVRIFRAEKSYTV
QSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFNGHRGQRWH
LGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIE
IGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRP
VTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQNSL
VEMLFLRLSLPVQFHQLNTTTYYYSVRVFAGQEPSCVWVGWVTPDYHQHD
MNFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVSPGQQGRISH
TDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNV
IQFELGKQMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFLQ
VETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHS
HTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDL
LISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRHGLPG
VGVTTSLRPPHHFSPPCFVAALPAAGVAEAPARLSPAIPLEALRDKALRM
LGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILK
MIEPEVFTEEDLEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAA
FAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLL
HFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIQLEKKPQSLQELVSHM
VVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVED
TMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRAL
GMHETVMEVMVNVLGGGETKEIRFPKMVTSCCRFLCYFCRISRQNQRSMF
DHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSY
LAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENAN
VVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDPARDGPRVHLGH
AIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVPLDDLVGII
SLPLQIPTQPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLP
DMRAAASLDTATFSTTEMALALNRYLCLAVLPTKCAPLFAGTEHRAIMVD
SMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDV
PILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFW
GIFDSLAHKKYDQELNFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAF
DKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIA
WEWTIEKAREGEYNPQPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQ
ELEAKGGGTHPLLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRGLK
DMELDTSSIEKRFAFGFLQQLLRWMDISQEFIAHLEHEQEIKFFAKILLP
LINQYFTNHCLYFLSTPAKVLHASNKEKEMITSLFCKLAALVRHRVSLFG
TDAPAVVNCLHILARSLRTVMSGPEIVKAGLRSFFESASEDIEKMVENLR
LGVGQNLTYTTVALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSI
YSLGTTKNTYKLRPALGECLARLAAAMPVAFLEPQLNEYNACVYTTKSPR
ERANSVEEMCPDIPVLDRLMADIGGLAESGARYPHVIEITLPMLCSYLPR
WWERGPEAPPAPPPCTVTSDHLNSLLGNILRIIVNNLGIDEATWMKRLAV
FAQPIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRLEEGELLVRD
EFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEELFRMVGEIFIYWS
KSHNFKREEQNFVVQNEINNMSFLQTSLIVATLKKMLPIGLNMCAPTDQD
LIMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSPSLRWQMALYRGLPG
REEDADDPEKIVRRVQEVSAVLYHLEQTEHPTPLYNLPTHRACNMFLESY
KAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLHQLVLHFSR
TALTEKSKLDEDYLYMAYADIMAKSCHLEEGGEEVEVSFEEKEMEKQRLL
YQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQ
KMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGT
VINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTIN
IIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNS
LTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLK
ELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDM
FLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSC
SEADENENFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLEL
AESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQ
FIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEPEFWGELEVQRVK
FLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPGDENMVYYFLEES
TGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDG
LYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRE
RIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGVIFT
DNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGK
QLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLF
HMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGL
IIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNL
ANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQ
LS

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 7t65 Chain D Residue 5101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7t65 Molecular mechanism of the severe MH/CCD mutation Y522S in skeletal ryanodine receptor (RyR1) by cryo-EM.
• Resolution: 4.05 Å
• Binding residue (original residue number in PDB): K4214 R4215 F4959 T4979 H4983
• Binding residue (residue number reindexed from 1): K3748 R3749 F4174 T4194 H4198
• 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:7t65, PDBe:7t65, PDBj:7t65
• PDBsum: 7t65
• PubMed: 35867837
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)