Structure of PDB 7m6a Chain B Binding Site BS04

Receptor Information

>7m6a Chain B (length=4306) Species: 9986 (Oryctolagus cuniculus)

VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPP
DLAICCFTLEQSLSVRALQEMLANHRTLLYGHAILLRHAHSRMYLSCLTT
SRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLF
HGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSH
LRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL
PKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKKA
ILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSGKPR
GSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQS
LFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLYELL
ASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPEVLN
IIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLL
PGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFLT
AQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGHV
ARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDGL
FFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRLEPI
KEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREKLAE
NIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSG
ETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVR
LTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRL
LDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVENQSRWDRVRIFR
AEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFNG
HRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSE
TAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPF
AINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRT
WGSQNSLVEMLFLRLSLPVQFHQHFRCTNRDDPEIILNTTTYYYSVRVFA
GQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCSN
CYMVWGGDFVRISHTDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTK
LFPAVFVLPTHQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEV
QMLMPVSWSRMPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRC
MDILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHA
LEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITL
FPPGRRHGLPGVGVTTSLRPPHHFSPPCFVAALAPARLSPAIPLEALRDK
ALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVK
QILKMIEPEVFTEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAF
AERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLLH
FKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIPQSLQELVSHMVVRWAQ
EDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLE
CLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETV
MEVMVNVLGIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSQG
STPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYP
DIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALR
GEGGSGLLAAIEEAIRISEDPARDGPNRVHLGHAIMSFYAALIDLLGRCA
PEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGALVQ
PKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASLD
TATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTVY
RLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEFA
KMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSLA
HKKYDQELYRMAMPCLCAIAGALPPDYVDASYSSKAEKNFDPRPVETLNV
IIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYK
TFSEKDKEIYRWPIKESLKAMIAWEWTIEKAREGEYNPQPPDLSGVTLSR
ELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARD
REKAQELLKFLQMNGYAVTRSSIEKRFAFGFLQQLLRWMDISQEFIAHLE
AVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGSG
GHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDAR
TVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKGVGQNLTYTTVALL
PVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTKNTYVEKLR
PALGECLARLAAAMPVAFLEPQLNEYNACSVYTTKSPRERAILGLPNSVE
EMCPDIPVLDRLMADIGGLAESGARYTEMPHVIEITLPMLCSYLPRWWER
GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEATWMKR
LAVFAQPIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRLEAKAEA
EEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEELFRM
VGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTYSVQTSLIVATLKKML
PIGLNMCAPTDQDLIMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSPS
LRWQMALYRGLPGREEDADDPEKIVRRVQEVSAVLYHLEQTEHPYKSLSK
QRRRAVVACFRMTPLYNLPTHRACNMFLESYKAAWILTEDHSFEDRMIDD
LSKAGEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLV
SFEEKEMEKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLG
ISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQN
KAEGLGMVNEDGTVIEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQ
TGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMS
VAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQD
SSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVE
MILKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGP
EIQFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPH
DPRLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWE
MPQVKESKRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEFWG
ELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPMVYYF
LEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKL
EFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDI
FGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFG
VIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVT
HNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMT
CYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAI
IQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLE
EHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQ
YEDQLS

Ligand information

• Ligand ID: CFF
• InChI: InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
• InChIKey: RYYVLZVUVIJVGH-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cn1cnc2N(C)C(=O)N(C)C(=O)c12
  ACDLabs 10.04: O=C2N(c1ncn(c1C(=O)N2C)C)C
  OpenEye OEToolkits 1.5.0: Cn1cnc2c1C(=O)N(C(=O)N2C)C
• Formula: C8 H10 N4 O2
• Name: CAFFEINE;
  3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE
• ChEMBL: CHEMBL113
• DrugBank: DB00201
• ZINC: ZINC000000001084
• PDB chain: 7m6a Chain B Residue 5304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m6a High-resolution structure of the membrane-embedded skeletal muscle ryanodine receptor.
• Resolution: 3.36 Å
• Binding residue (original residue number in PDB): E4239 W4716 I4996 W5011
• Binding residue (residue number reindexed from 1): E3833 W3985 I4265 W4280
• 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:7m6a, PDBe:7m6a, PDBj:7m6a
• PDBsum: 7m6a
• PubMed: 34469755
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)