Structure of PDB 5gkz Chain E Binding Site BS01

Receptor Information

>5gkz Chain E (length=3660) Species: 9986 (Oryctolagus cuniculus)

QFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPD
LAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTT
SRKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSE
RYLHLSTLQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGECLTIS
AADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRH
VTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKLKRDVEGMGPPE
IKYGESLCFVQHVASGLWLTYAAVLKKKAILHQEGHMDDALFLTRCQQEE
SQAARMIHSTAGLYNQFIKGLDSFSGKPRLPIEAVILSLQDLIGYFEPPS
EELQHEEKQSKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTYAGEEAA
ESWKEIVNLLYELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILE
VLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGV
AVRSNQDLITENLLPGRELLLQTNLINYVTSIRPNIFVGGKWYFEVMVDE
VVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLH
LWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEA
FNLDGLFFPVVSFSAGVKVRFLLGEFKFLPPPGYAPCHEAVLPRERLRLE
PIKEYRREGPRGPHLVGPSRCFVPCPVDTVQIVLPPHLERIREKLAENIH
ELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETL
KTLLALGCHVGMADEKAYMMSNGYKPAPLDLSHVRLTPAQTTLVDRLAEN
GHNVWARDRVAQRRNPRLVPYRLLDEATKRSNRDSLCQAVRTLLGYGYNI
EPRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGAD
ELAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEV
LAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPF
AINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDLAHRTWGSQNSLVEM
LFLRLSLPVQFTYYYSVRVFACVWVGWVTPDYHQHDMNFDLSVTVTMGDE
QGNVHSSLKCSNYMVWGSHTDLVIGCLVGLMTFTANGKESNTFFQVEPNT
KLFPAVFVLPTHQNVIQFEAAMFLSERKNPAPQCPPRLEVQMLMPVSWSR
MPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERL
DLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPL
RAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGLPGVGV
TTSLRPPHHFSPPCFVALSPAIPLEALRDKALRMLGEAVRDGGQHARDPV
GGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEGLLQMKLPESV
KLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRDFHQDLLAH
CGIQLETSLSSRLRSLLETVRLSLQELVSHMVVRWAQEDYVQSPELVRAM
FSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQE
ENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGPKMVTSCC
RFLCYFCRISRQNQRSMFDHLSYLLENSGITPLDVAAASVIDNNELALAL
QEQDLEKVVSYLAGCGLPCGGERYLDFLRFAVFVNGESVEENANVVVRLL
IRKPEGLLAAIEEAIRIGHAIMSFYAALIDLLGRCAEALRIRAILRSLLD
DLVGIISLPLQIFVPDHKASMVLFLDRVYNQDFLLHVLVGFLPDMRAAAS
LTEMALALNRYLCLAVLPLIPLFAGTEHRAIMVDSMLHTVRGRSLTKAQR
DVIEDCLMARPSMLQHLLRRLVFDVPILNKMPLKLLTNHYERCWKYYCLP
TGTSEEELHLTRKLFWGIFDSLYDQELYRMAMPCLCAIAGALPPNFDPRP
VETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHP
MLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIEKAREGEYDPREGYNP
QPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVP
YDTLTAKEKARDREKAQELLKFLQMNGYAVTRGYFLSTPAKVLGSGGHAS
NKEKEMIFCKLAALVRHRVSLFGTDAPLHILARSLDARTVMKSGPEIVKA
FFESASEDIEKMVENLRLGKVSTTVALLPVLTTLFQHIAQHQFLDDVQVS
CYRTLCSIYSLGTTVEKLRPALGECLARLAAAAFLEPQLNEYNACSTLPM
LCSYLPRWWERGPEPALPAGAPPPCTAVTSDHLNGNILRIIVNNLGIDEA
TWMKRLAVSRARPELLHSHFIPTIGKRAGKVVAEEEQLRLEAKAEAEEGE
LLVRDECRDLYALYPLLIRYVDNNRAHWLPNANAEELFMVGEIFIYWSKS
HNFKREENFVVQNEINNMSFLMAKAGDAQSGGSDQTKKKRRGDRYSTLKK
MLPIGLNMCAPKTRYALKDVREFLQNNLHLQGKVEGSPSLRWQPTHRACN
MFLESYKAAWILTEDHSFEDRMIDDLSKAKPDPLHQLVLHFSRTALTEKS
KLDEDYLYMAYADIMAKSCEVSFEEKEMEKQRLLYQQSRLHTRGAAEMVL
QMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQ
SIQALMQTCSVLDLNAFERQNKDDEFTQDLFRFLQLLCEGHNNDFQNYLR
TQTGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKA
MSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLA
QDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSN
VEMILKFFDMIVGSEAFQDYVTDPRGLISKKDFQKAMDSQQFTGPEIQFL
LSCSEADENEMINFEEFANRPARDIGFNVAVLLTNLSEHVPHDPRLRNFL
ELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESK
RQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQIEVQRVKFLNYLSR
NFYTLRFLALFLAFAINFILLFYKVSVYYFLEESTGYMEPALWCLSLLHT
LVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPGDDDVKGQW
DRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGLTWLMSIDV
KYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTL
RTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPD
MKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFF
VIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPH
GFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFP
AGDCFRKQYE

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5gkz Chain E Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gkz The Central domain of RyR1 is the transducer for long-range allosteric gating of channel opening
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): C4958 C4961 H4978 H4983
• Binding residue (residue number reindexed from 1): C3585 C3588 H3605 H3610
• 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:5gkz, PDBe:5gkz, PDBj:5gkz
• PDBsum: 5gkz
• PubMed: 27468892
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)