Structure of PDB 5gl1 Chain G Binding Site BS01

Receptor Information

>5gl1 Chain G (length=3645) 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
KLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRTSLSSRLRS
LLETVRLSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELL
RALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQEENLMIQSIGNIMNNK
VFYQHPNLMRALGMHETVMEVMVNVLGPKMVTSCCRFLCYFCRISRQNQR
SMFDHLSYLLENSGITPLDVAAASVIDNNELALALQEQDLEKVVSYLAGC
GLPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPEGLLAAIEEAI
RIGHAIMSFYAALIDLLGRCAEALRIRAILRSLLDDLVGIISLPLQIFVP
DHKASMVLFLDRVYNQDFLLHVLVGFLPDMRAAASLTEMALALNRYLCLA
VLPLIPLFAGTEHRAIMVDSMLHTVRGRSLTKAQRDVIEDCLMARPSMLQ
HLLRRLVFDVPILNKMPLKLLTNHYERCWKYYCLPTGTSEEELHLTRKLF
WGIFDSLYDQELYRMAMPCLCAIAGALPPNFDPRPVETLNVIIPEKLDSF
INKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEI
YRWPIKESLKAMIAWEWTIEKAREGEYDPREGYNPQPPDLSGVTLSRELQ
AMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDREK
AQELLKFLQMNGYAVTRGYFLSTPAKVLGSGGHASNKEKEMIFCKLAALV
RHRVSLFGTDAPLHILARSLDARTVMKSGPEIVKAFFESASEDIEKMVEN
LRLGKVSTTVALLPVLTTLFQHIAQHQFLDDVQVSCYRTLCSIYSLGTTV
EKLRPALGECLARLAAAAFLEPQLNEYNACSTLPMLCSYLPRWWERGPEP
ALPAGAPPPCTAVTSDHLNGNILRIIVNNLGIDEATWMKRLAVSRARPEL
LHSHFIPTIGKRAGKVVAEEEQLRLEAKAEAEEGELLVRDECRDLYALYP
LLIRYVDNNRAHWLPNANAEELFMVGEIFIYWSKSHNFKREENFVVQNEI
NNMSFLMAKAGDAQSGGSDQTKKKRRGDRYSTLKKMLPIGLNMCAPKTRY
ALKDVREFLQNNLHLQGKVEGSPSLRWQPTHRACNMFLESYKAAWILTED
HSFEDRMIDDLSKAKPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIM
AKSCEVSFEEKEMEKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVS
STLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLN
AFERQNKDDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICT
VDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYI
QGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDL
QKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMIVGSE
AFQDYVTDPRGLISKKDFQKAMDSQQFTGPEIQFLLSCSEADENEMINFE
EFANRPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLG
RIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAE
KMELFVSFCEDTIFEMQIAAQIEVQRVKFLNYLSRNFYTLRFLALFLAFA
INFILLFYKVSVYYFLEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKV
PLVIFKREKELARKLEFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYW
DKFVKRKVLDKHGDIFGRERIAELLGLTWLMSIDVKYQIWKFGVIFTDNS
FLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLV
MTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMY
VGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIID
AFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANY
MFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYE

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: 5gl1 Chain G Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gl1 The Central domain of RyR1 is the transducer for long-range allosteric gating of channel opening
• Resolution: 5.7 Å
• Binding residue (original residue number in PDB): I4960 C4961 H4983
• Binding residue (residue number reindexed from 1): I3572 C3573 H3595
• 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:5gl1, PDBe:5gl1, PDBj:5gl1
• PDBsum: 5gl1
• PubMed: 27468892
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)