Structure of PDB 7k0t Chain B Binding Site BS01

Receptor Information
>7k0t Chain B (length=4105) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPD
LAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTT
SRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLF
HGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSH
LRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL
DTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLK
KKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSG
KPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRN
RQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLY
ELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPE
VLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITE
NLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVP
FLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWT
GHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNL
DGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRL
EPIKEYRREGPRGPHLVGPSRCLSHTDFHLERIREKLAENIHELWALTRI
EQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETLKTLLALGC
HVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVRLTPAQTTLVDR
LAENGHNVWARDRVAQGWSPYRLLDEATKRSNRDSLCQAVRTLLGYGDRV
RIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAY
VFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSD
SGSETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEG
FEPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRL
AHRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHF
LQVWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHSHTLRLYRA
VCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDLLISIHLES
ACRSRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRHGLPGVGVTTSLR
PPHHFSPPCFVAAAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPV
GGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEEEELEEG
LLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRS
RYALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDEADEEDCPLPE
DIRQDLQDFHQDLLAHCGIQLEGKKPQSLQELVSHMVVRWAQEDYVQSPE
LVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSL
LIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVL
GGGETKEIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGIGL
GMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLA
KGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFG
PALRGEGGSGLLAAIEEAIRISEDRVHLGHAIMSFYAALIDLLGRCAPEM
HLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAANFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSY
GENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEELQAMAE
QLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDREKAQEL
LKFLQMNGYAVTRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATPLYNLPTHRA
CNMFLESYKAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLH
QLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGVEVSFEEKEM
EKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGG
NAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGM
VNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTG
NTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVA
KQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSS
QIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMI
LKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEI
QFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDP
RLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMP
QVKESKRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEFWGEL
EVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPNMVYYFL
EESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLE
FDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIF
GRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGV
IFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTH
NGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTC
YLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAII
QGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEE
HNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQY
EDQLS
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
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)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain7k0t Chain B Residue 5101 [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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PDB7k0t Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		M4954 C4958 N4984 L4985
Binding residue
(residue number reindexed from 1)		M4022 C4026 N4052 L4053
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Feb 21 18:12:33 2025

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()
   1435     title=pdb2title(pdbid)
   1436     if bs.startswith("BS"):
=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1438     else:
   1439         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '7k0t', asym_id = 'B', bs = 'BS01', title = 'Ca 2+ -inactivation of the mammalian ryanodine r...e 1 in a lipidic environment revealed by cryo-EM.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7k0t', asym_id='B', bs='BS01', title='Ca 2+ -inactivation of the mammalian ryanodine r...e 1 in a lipidic environment revealed by cryo-EM.')
   1295         display_ec(ec,csaOrig,csaRenu)
   1296     if go:
=> 1297         display_go(go,uniprot,pdbid,asym_id)
   1298     return pubmed,uniprot
   1299 
global display_go = <function display_go>, go = '0005216,0005219,0005262,0006811,0006816,0006874,0016020,0055085,0070588', uniprot = '', pdbid = '7k0t', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005216,0005219,0005262,0006811,0006816,0006874,0016020,0055085,0070588', uniprot='', pdbid='7k0t', asym_id='B')
    480         '''.replace("$namespace_link",namespace_link
    481           ).replace("$namespace",namespace
=>  482           ).replace("$uniprot",u
    483         ))
    484         for l,(term,name) in enumerate(go2aspect[Aspect]):
u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>