Structure of PDB 7tdk Chain D Binding Site BS03

Receptor Information

>7tdk Chain D (length=4134) Species: 9986 (Oryctolagus cuniculus)

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 ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 7tdk Chain D Residue 5103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7tdk Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): E3893 E3967 T5001
• Binding residue (residue number reindexed from 1): E3314 E3388 T4098
• Annotation score: 5

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:7tdk, PDBe:7tdk, PDBj:7tdk
• PDBsum: 7tdk
• PubMed: 35257661
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)