Structure of PDB 8vk4 Chain A Binding Site BS05

Receptor Information
>8vk4 Chain A (length=4379) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVP
PDLAICCFILEQSLSVRALQEMLANHRTLLYGHAILLRHAHSRMYLSCLT
TSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILV
SVSSERYLHLSTASGELQVDASFMQTLWNMNPICSGCEEGFVTGGHVLRL
FHGHMDECLTISPSDSDDQRRLVYYEGGPVCTHARSLWRLEPLRISWSGS
HLRWGQPLRIRHVTTGRYLGLTEDQGLVVVDASKAHTKATSFCFRISKEK
LDVAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVL
KKKAMLHQEGHMDDALSLTRCQQEESQAARMIYSTAGLYNQFIKGLDSFS
GKPRGSGPPAGSALPIEGVILSLQDLIGYFEPPSEELQHEEKQTKLRSLR
NRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEFAGEEAAESWKEIVNLL
YELLASLIRGNRTNCALFSTNLDWLVSKLDRLEASSGILEVLYCVLIESP
EVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLIT
ENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVA
PFLTAQATHLRVGWALSEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLW
TGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFESFN
LDGLFFPVVSFSAGIKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLH
LQPIKEYRREGPRGPHLVGPSRCLSHLDFVPCPVDTIQIVLPPHLERIRE
KLAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNL
QMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDL
SHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLV
PYRLLDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVDSQSRGDRA
RIFRAEKSYAVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADDLAY
VFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSD
SGSETAFRDIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEG
FEPFAINMQRPVTTWFSKSLPQFEPVPLEHPHYEVARMDGTVDTPPCLRL
THRTWGSQNSLVEMLFLRLSLPVQFHQHFRCTDNRDDPEIILNTTTYYYS
VRVFAGQEPSCVWVGWVTPDYHQHDMSFDLSKVRAVTVTMGDEQGNVHSS
LKCSNCYMVWGGDFVSPGQQGRISHTDLVIGCLVDLATGLMTFTANGKES
NTFFQVEPNTKLFPAVFVLPTHQNVVQFELGKQKNIMPLSAAMFLSERKN
PAPQCPPRLEVQMLMPVSWSRMPNHFLQVDTRRAGERLGWAVQCQEPLMM
MALHIPEENRCMDILELSERLDLQRFHSHTLSLYRSVCALGNNRVAHALC
SHVDQAQLLHALEDARLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIV
PLTPETRAITLFPPGRSAEDGPRRHGLPGVGVTTSLRPPHHFSPPCFVVA
LPAAGATEAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVE
FQFVPVLKLVSTLLVMGVFSDEDVKQILKMIEPEVFREELEEGLLQMKLP
ESVKLQMCHLLEYFCDQELQHRVESLAAFAECYVDKMQGNQRGRYGLLMK
AFTMSAAETARRTREFRSPPQEQINMLLHFKNGADEEECPLPEEIRQELV
NFHQDLLAHCGIQLEHKPQSLQELVSHTVVRWAQEDFVQSPELVRAMFSL
LHRQYDGLGELLRALPRAYTISVSSVEDTMSLLECLGQIRSLLIVQMGPQ
EENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGGGESKEI
RFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGIGLGMQGSTPL
DVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGW
NPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGEGG
SGLLAAIEEAIRISEDPARDGPGVPPEENRVHLGHAIMSFYAALIDLLGR
CAPETHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGAL
VQPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAAS
LDTATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHT
VYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNE
FAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDS
LAHKKYDQELYRIAMPCLCAIAGALPPDYVDASYSSKTEKNFDPRPVETL
NVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENIDEELKTHPMLRP
YKTFSEKDKEIYRWPIKESLKAMIAWEWTVEKAREGEYNPQPPDLSVVTL
SRELQAMAEQLAENYHNTWGRKKKQELEAKGGGSHPLLVPYDTLTAKEKA
RDREKAQELLKFLQMNGYAVTRGLKDMELDTSSIEKRFAFGFLQQLLRWM
DISQEFIAHLEAVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYF
LSTPAKVLGSGGHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNC
LHILARSLDARTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLKGVGQ
NLTYTTVALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGT
TRNPYVEKLRPALGECLARLAAAMPVAFLEPELNEYNACSVYTTKSPRER
AILGLPNSVEEMCPDIPVLERLMAEIGGLAESGARYTEMPHVIEITLPML
CSYLPRWWERGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNL
GIDEASWMKRLAVFAQPIVSRARPELLRSHFIPTIGRLRKRAGKVVAEEE
QLRLEAKAEAEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEP
NPNAEELFRMVGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTYSVQTS
LIVATLKKMLPIGLNMCAPTDQDLIVLAKARYALKDTDEEVREFLQNNLN
LQGKVEGSPSLRWQMALYRGVPGREEDADDPEKIVRRVQEVSAVLYHLDQ
TEHPRRRAVVACFRMTPLYNLPTHRACNMFLESYKASWILTEDHSFEDRM
IDDLSKAGEQEEEEEEVEEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYM
AYADIMAKSCHLEVEVSFEEKEMEKQRLLYQQSRLHNRGAAEMVLQMISA
CKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQAL
MQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLF
RFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQESISDFYW
YYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRL
WDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNV
VNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQDYVTDPR
GLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINCEEFANRFQEP
ARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLGRIEIMG
ASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGESEKMEMFV
SFCEDTIFEMQIAAQISEPFWGELEVQRVKFLNYLSRNFYTLRFLALFLA
FAINFILLFYKVSDSPPNMVYYFLEESTGYMEPALRCLSLLHTLVAFLCI
IGYNCLKVPLVIFKREKELARKLEFDGLYITEQPEDDDVKGQWDRLVLNT
PSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGMDLASLEITAHNERKP
DPPPGLLTWIMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFF
FAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNF
FRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDE
YELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKC
FICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQES
YVWKMYQERCWDFFPAGDCFRKQYEDQLS
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8vk4 Chain A Residue 8005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8vk4 Structural insights into the regulation of RyR1 by S100A1.
Resolution3.56 Å
Binding residue
(original residue number in PDB)		W883 R898 E918 M925 W997 R1021
Binding residue
(residue number reindexed from 1)		W860 R875 E895 M902 W974 R998
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0002020 protease binding
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:0019899 enzyme binding
GO:0046872 metal ion 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:0006937 regulation of 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:0030314 junctional membrane complex
GO:0030315 T-tubule
GO:0031090 organelle membrane
GO:0032991 protein-containing complex
GO:0033017 sarcoplasmic reticulum membrane
GO:1990425 ryanodine receptor complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8vk4, PDBe:8vk4, PDBj:8vk4
PDBsum8vk4
PubMed38917010
UniProtE9PZQ0|RYR1_MOUSE Ryanodine receptor 1 (Gene Name=Ryr1)

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