Structure of PDB 8vk4 Chain D Binding Site BS01

Receptor Information

>8vk4 Chain D (length=4379) Species: 10090 (Mus musculus)

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 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: 8vk4 Chain D Residue 8001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vk4 Structural insights into the regulation of RyR1 by S100A1.
• Resolution: 3.56 Å
• Binding residue (original residue number in PDB): C4956 C4959 H4976 H4981
• Binding residue (residue number reindexed from 1): C4300 C4303 H4320 H4325
• Annotation score: 1

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

External links

• PDB: RCSB:8vk4, PDBe:8vk4, PDBj:8vk4
• PDBsum: 8vk4
• PubMed: 38917010
• UniProt: E9PZQ0|RYR1_MOUSE Ryanodine receptor 1 (Gene Name=Ryr1)