Structure of PDB 7tdk Chain B Binding Site BS01

Receptor Information
>7tdk Chain B (length=4134) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPD
LAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTT
SRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLF
HGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSH
LRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL
DTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLK
KKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSG
KPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRN
RQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLY
ELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPE
VLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITE
NLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVP
FLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWT
GHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNL
DGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRL
EPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREK
LAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQ
MSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLS
HVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSVPYRLLDEATKRSNR
DSLCQAVRTLLGYGYNIEDRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMR
VGWARPELRPDVELGADELAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGC
MIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLGPGQVGH
LNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPPE
HPHYEVARMDGTVDTPPCLRLAHRAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAMPLSAAMFLSERKNPAPQC
PPRLEVQMLMPVSWSRMPNHFLQVETRRGWAVQCQDPLTMMALHIPEENR
CMDILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLH
ALEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAIT
LFPPGRKGGNARRHGLPGVGVTTSLRPPHHFSPPCFVAALEAPARLSPAI
PLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMG
IFGDEDVKQILKMIEPEVFTEELEEGLLQMKLPESVKLQMCNLLEYFCDQ
ELQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFR
SPPQEQINMLLHFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIQLEGK
KPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLRALP
RAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNK
VFYQHPNLMRALGMHETVMEVMVNVLGGGETKEIRFPKMVTSCCRFLCYF
CRISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALA
LQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAV
FVNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISED
PARVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVP
LDDLVGIISLPLQIPTLAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANFDPRPVETLNVIIPE
KLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSE
KDKEIYRWPIKESLKALSRELQAMAEQLAENYHNTWGRKKKQELEAKGGG
THPLLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAATPLYNLPTHRACNMFLESYKAAWILTEDHSFEDRM
IDDLSKAGEQEEEEEEVEEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYM
AYADIMAKSCHLEEGGEEEVEVSFEEKEMEKQRLLYQQSRLHTRGAAEMV
LQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFF
QSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDE
FTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQES
ISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQS
LAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLS
LLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQD
YVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINFEEFA
NRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLG
RIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAE
KMELFVSFCEDTIFEMQIAAQISEFWGELEVQRVKFLNYLSRNFYTLRFL
ALFLAFAINFILLFYKVSDSPPNMVYYFLEESTGYMEPALWCLSLLHTLV
AFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPGDDDVKGQWDR
LVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGMDLASLEITAH
NERKPDPPPGLLTWLMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGH
YNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTV
VAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIED
PAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKED
METKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEH
TGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain7tdk Chain B Residue 5101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7tdk Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		R4215 C4958 F4959
Binding residue
(residue number reindexed from 1)		R3636 C4055 F4056
Annotation score1
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7tdk, PDBe:7tdk, PDBj:7tdk
PDBsum7tdk
PubMed35257661
UniProtP11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)

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