Structure of PDB 6m2w Chain D

Receptor sequence

>6m2wD (length=3949) Species: 9986 (Oryctolagus cuniculus)

QFLRTDDEVVLQCSAEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAIC
CFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTTSRSM
TDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSE
RYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHECL
TISAQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVT
TGRYLALVVVDACKAHTKATSFCFRVSKEKLGMGPPEIKYGESLCFVQHV
ASGLWLTYALKKKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYN
QFIKGLDSFSGKPRGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKL
RSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEI
VNLLYELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVL
IESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQ
DLITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMV
DEVVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDG
LHLWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVF
EAFNLDGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPR
ERLRLEPIKEYRREGPRPHLVGPSRCLSHTDFVPCPIVLPPHLERIREKL
AENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQM
SGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSH
VRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPY
RLLDEATKRSNRDSLCQAVRTLLGYGYNIEPDRVRIFRAEKSYTVQSGRW
YFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFNGHRGQRWHLGSEP
FGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGF
LPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWF
SKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQNSLVEMLF
LRLSLPVQFHQHFRCDDPEIILNTTTYYYSVRVFAGQEPSCVWVGWVTPD
YHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVISHTD
LVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVIQ
FELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFL
QVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFH
SHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYD
LLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRRHGLPGVGVTT
SLRPPHHFSPPCFVAALPAEAPARLSPAIPLEALRDKALRMLGEAVRDGG
QHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTE
EEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQAN
QRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDDCPLPEDI
RQDLQDFHQDLLAHCGIQLEPQSLQELVSHMVVRWAQEDYVQSPELVRAM
FSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQM
GPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGEIRF
PKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGMQGSTPLDVAAAS
VIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGE
RYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGSGLLAAIEE
AIRISEDPARDGPNRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEA
LRIRAILRSLVPLDDLVGIISLPLQIPTLVQPKMSASFVPDHKASMVLFL
DRVYGIENQDFLLHVLDVGFLPDMRAAASLDTEMALALNRYLCLAVLPLI
TKCAPLFAGTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCR
YIRPSMLQHLLRRLVFDVPILNAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAETLNVIIPEKLDSFINKFAEYTHEKWAF
DKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIA
WEWTIEKAREGEYNPQPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQ
ELEALVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAALLSKQRRRAVVACFRMTPLYNLPTHRACNM
FLESYKAAWILTEDHSFEDRMIDDLSKAGEQEKKPDPLHQLVLHFSRTAL
TEKSKLDEDYLYMAYADIMAKSCHLEEEVSFEEKEMEKQRLLYQQSRLHT
RGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKD
KKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGE
KVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDY
LLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGP
CTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKD
MVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIV
GSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEM
INFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILE
YFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVV
NEGGEAEKMELFVSFCEDTIFEMQIAAQISEAAAAAAAAAAAAAAAAAAA
AAWGELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPN
MVYYFLEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKE
LARKLEFDGLYITEQPDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHG
DIFGRERIAELLGMDLASLEITAHNERTWLMSIDVKYQIWKFGVIFTDNS
FLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLV
MTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMY
VGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIID
AFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANY
MFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

3D structure

• PDB: 6m2w Structural basis for diamide modulation of ryanodine receptor.
• Chain: D
• Resolution: 3.8 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CFF	D	F3753 W4716 I4996 Y5014	F2981 W3637 I3908 Y3926
BS02	CA	D	E3893 E3967 Q3970 T5001 E5002 H5003	E3121 E3195 Q3198 T3913 E3914 H3915
BS03	ATP	D	K4214 M4954 K4957 C4958 T4979 H4983 N4984	K3442 M3866 K3869 C3870 T3891 H3895 N3896
BS04	ZN	D	H4978 H4983	H3890 H3895
BS05	F0U	D	R4563 F4564 Y4791 L4792 D4815 I4816 M4818 G4819	R3525 F3526 Y3703 L3704 D3727 I3728 M3730 G3731

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:6m2w, PDBe:6m2w, PDBj:6m2w
• PDBsum: 6m2w
• PubMed: 32807966
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)