Structure of PDB 7tdh Chain B Binding Site BS02

Receptor Information

>7tdh Chain B (length=4165) Species: 9986 (Oryctolagus cuniculus)

QFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPD
LAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTT
SRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLF
HGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSH
LRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL
DTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLK
KKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSG
KPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRN
RQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLY
ELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPE
VLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITE
NLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVP
FLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWT
GHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNL
DGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRL
EPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDIVLPPHLERIREKLAE
NIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSG
ETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVR
LTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVPYRLLDEATKRSNRDS
LCQAVRTLLGYGYNIEDRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVG
WARPELRPDVELGADELAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMI
DLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLGPGQVGHLN
LGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPPEHP
HYEVARMDGTVDTPPCLRLAHRAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAMPLSAAMFLSERKNPAPQCPP
RLEVQMLMPVSWSRMPNHFLQVERLGWAVQCQDPLTMMALHIPEENRCMD
ILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALE
DAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFP
PGRKGGNARRHGLPGVGVTTSLRPPHHFSPPCFVAALPAEAPARLSPAIP
LEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGI
FGDEDVKQILKMIEPEVFTEELEEGLLQMKLPESVKLQMCNLLEYFCDQE
LQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRS
PPQEQINMLLHFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIQLEGKK
PQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLRALPR
AYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKV
FYQHPNLMRALGMHETVMEVMVNVLGGGETKEIRFPKMVTSCCRFLCYFC
RISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALAL
QEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVF
VNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDP
ARDGPNRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILR
SLVPLDDLVGIISLPLQIPTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANFDPRPVETLNVI
IPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKT
FSEKDKEIYRWPIKESLKAMIAWEWTIEKAREGEYNPQPPDLSGVTLSRE
LQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDR
EKAQELLKFLQMNGYAVTRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATPLYN
LPTHRACNMFLESYKAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEK
KPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGENEE
VEVSFEEKEMEKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTL
KLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFE
RQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNND
FQNYLRTQTGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGK
RNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAH
MMMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDML
VESSSNVEMILKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMD
SQKQFTGPEIQFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLT
NLSEHVPHDPRLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEIS
ETNRAQWEMPQVKESKRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIA
AQISEFWGELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSD
SPPNMVYYFLEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFK
REKELARKLEFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKR
KVLDKHGDIFGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSID
VKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKT
LRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEP
DMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFF
FVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTP
HGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFF
PAGDCFRKQYEDQLS

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: 7tdh Chain B Residue 5102

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7tdh Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): E3893 T5001
• Binding residue (residue number reindexed from 1): E3345 T4129
• 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:7tdh, PDBe:7tdh, PDBj:7tdh
• PDBsum: 7tdh
• PubMed: 35257661
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)