Structure of PDB 6jii Chain B

Receptor sequence

>6jiiB (length=3508) Species: 9823 (Sus scrofa)

QFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVPPD
LSICTFVLEQSLSVRALQEMLANGHRTLLYGHAILLRHSYSGMYLCCLST
SRKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILVSVSSE
RYLHLSYLHVDAAFQQTLWSVAPISSAQGYLIGGDVLRLLHGECLTVPSG
EHEQRRTVHYEGGAVSVHARSLWRLETLRVAWSGSHIRWGQPFRLRHVTT
GKYLSLMEDKSLLLMDKEKADVKSTAFTFRSSKEKLRKEVDGMGTSEIKY
GDSVCFIQHIGTGLWLTYQSSIQRKAIMHHEGHMDDGLNLSRSQHEESRT
ARVIRSTVFLFNRFIRGLDALSKKAKTVDLPIESVSLSLQDLIGYFHPPD
EHLEHEDKQNRLRALKNRQNLFQEEGMINLVLECIDRLHVYSSVAGREAG
ESWKSILNSLYELLAALIRGNRKNCAQFSGSLDWLISRLERLEASSGILE
VLHCVLVESPEALNIIKEGHIKSIISLLDKHGRNHKVLDVLCSLCVCHGV
AVRSNQHLICDNLLPGRDLLLQTRLVNHVSSMRPNIFLGKKWYYELMVDH
TEPFVTAEATHLRVGWASTEGYSPYPGGGEEWGGNGVGDDLFSYGFDGLH
LWSGCIARTVSSPNQHLLRTDDVISCCLDLSAPSISFRINGQPVQGMFEN
FNIDGLFFPVVSFSAGIKVRFLLGEFKFLPPPGYAPCYEAVLPKEKLKVE
HSREYKQERTYTRDLLGPTVSAFTPIPVDTSQIVLPPHLERIREKLAENI
HELWVMNKIELGWQYGPVRDDNKRQHPCLVEFSKLPEQERNYNLQMSLET
LKTLLALGCHVGISDEHAYQLTSGYKPAPMDLSFIKLTPSQEAMVDKLAE
NAHNVWARDRIRQRRNPRLVPYALLDDRTKKSNKDSLREAVRTLLGYGYN
LEARFRIFRAEKTYAVKAGRWYFEFEAVTAGDMRVGWSRPGCQPDQELGS
DERAFAFDGFKAQRWHQGNEHYGRSWQAGDVVGCMVDMTEHTMMFTLNGE
ILLDDSGSELAFKDFDVGDGFIPVCSLGVAQVGRMNFGKDVSTLKYFTIC
GLQEGYEPFAVNTNRDITMWLSKRLPQFLQVPSSHEHIEVTRIDVTQKSF
GSQNSSTDIMFYRLSMPIECTYYYSVRIFPNVWVGWITSDFHQYDTAFDL
VTVTLGDEKGKVHESIKRSNYMVCANNNGLEIGCVVGLLTFTANGKDLST
YYQVEPSTKLFPAVFAQATSPNVFQFEAGLFKSEHKNPVPQCPPRLHVQF
LSHVLWSRMPNQFLKVDVSRISERQGWLVQCLEPLQFMSLHIPEENRSVD
ILELTEQEELLKFHYHTLRLYSAVCALGNHRVAHALCSHVDEPQLLYAIE
NKYMPGLLRAGYYDLLIDIHLSSYATARLMMNNEFIVPMTEETKSITLFP
DENKKHGLPGIGLSTSLRPRMQFSSPSFVSINNECYQYSPEFPLDILKAK
TIQMLTEAVQEGSLHARDPVGGTTEFLFVPLIKLFYTLLIMGIFHNEDLK
HILQLIEPSGLLQMKLPEPVKLQMCLLLQYLCDCQVRHRIEAIVAFSDDF
VAKLQDNQRFRYNEVMQALNECPCPEEIRDQLLDFHEDLMTHCGIELDLT
IRGRLLSLVEKVTYTLQQLISETMVRWAQESVIEDPELVRAMFVLLHRQY
DGIGGLVRALPKTYTINGVSVEDTINLLASLGQIRSLLSVEEEKLMIRGL
GDIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGPKMVANCCRFLCYFCR
ISRQNQKAMFDHLSYLLENSSVGLASPAMRGSTPLDVAAASVMDNNELAL
ALREPDLEKVVRYLAGCGLPVEGERYLDFLRFAVFCNGESVEENANVVVR
LLIRRPEGLLAAMEEAIKIGNAIMTFYAALIDLLGRCAPEMHLIHAAKGE
AIRIRSILRSLIPLGDLVGVISIAFQFCPDHKAAMVLFLDRVYVQDFLLH
LLGFLPDLRAAASLTDMALALNRYLCTAVLPLLAGTEHHASLIDSLLHTV
KGCSLTKAQRDSIEVCLLSRPSMMQHLLRRLVFDVPLLNKMPLKLLTNHY
ERCWKYYCLPGGASEEELHLSRKLFWGIFDALYEQELFKLALPCLSAVAG
ALPPNFNPQPVDTSNITIPEKLEYFINKYAEHSHDKWSMDKLANGWIYGE
IYSDSSKVQPLMKPYKLLSEKEKEIYRWPIKESLKTMLAWGWRIERTREG
DAAHGYSPRAIDMSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELESKGG
GNHPLLVPYDTLTAKEKAKDREKAQDILKFLQINGYAVSRGYFLSAASRP
LCSGGHASNKEKEMVFCKLGVLVRHRISLFGNDATLHILGQTLDARTVMK
TGLESVKFLDNAAEDLEKTMENLKQGQFTTTVALLPMLSSLFEHIGQHQF
LEDVQVSCYRILTSLYALGTSVERQRSALGECLAAFAGAAFLETHLDKHN
IYSSKQRKRAVVACFRMAPLYNLPRHRAVNLFLQGYEKSWIETEEHYFED
KLIEDLAKPRVDPLHQLILLFSRTALTEKCKLEEDFLYMAYADIMAKSCS
FEEKEMEKQKLLYQQARLHDRGAAEMVLQTISASKGETGPMVAATLKLGI
AILNGGNSTVQQKMLEYLKEKKDVGFFQSLAGLMQSCSVLDLNAFERQNK
AEGLGMKVLQDDEFTCDLFRFLQLLCEGHNSDFQNYLRTQTGNNTTVNII
ISTVDYLLRVQESISDFYWYYSGKDVIDEQGQRNFSKAIQVAKQVFNTLT
EYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMQMKLSQDSSQIELLKEL
MDLQKDMVVMLLSMLEGNVVNGTIGKQMVDMLVESSNNVEMILKFFDMFL
KLKDLTSSDTFKEYDPDGKGVISKRDFHKAMESHKHYTQSETEFLLSCAE
TDENETLDYEEFVKRFHEPAKDIGFNVAVLLTNLSEHMPNDTRLQTFLEL
AESVLNYFQPFLGRIEIMGSAKRIERVYFEISESSRTQWEKPQVKESKRQ
FIFDVVNEGGEKEKMELFVNFCEDTIFEMQLAAQIIAYQQKLLNYFARNF
YNMRMLALFVAFAINFILLFYKVSVHYVLEESSGYMEPTLRILAILHTVI
SFFCIIGYYCLKVPLVIFKREKEVARKLEFDGLYITEQPSEDDIKGQWDR
LVINTQSFPNNYWDKFVKRKVMDKYGEFYGRDRISELLGSAVLNSIDVKY
QMWKLGVVFTDNSFLYLAWYMTMSVLGHYNNFFFAAHLLDIAMGFKTLRT
ILSSVTHNGKQLVLTVGLLAVVVYLYTVVAFNFFRKFYNKSEDGDTPDMK
CDDMLTCYMFHMYVGVRAGGGIGDEIEDPAGDEYEIYRIIFDITFFFFVI
VILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGNDYFDTVPHGF
ETHTLQEHNLANYLFFLMYLINKDETEHTGQESYVWKMYQERCWEFFPAG
DCFRKQYE

3D structure

• PDB: 6jii Modulation of cardiac ryanodine receptor 2 by calmodulin.
• Chain: B
• Resolution: 4.2 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	B	C4889 C4892 H4914	C3433 C3436 H3458
BS02	CA	B	E3923 Q3926 T4932	E2801 Q2804 T3476
BS03	CFF	B	W4646 I4927 Y4945	W3213 I3471 Y3489
BS04	ATP	B	K4167 K4170 M4885 K4888 C4889 F4890 T4910	K3045 K3048 M3429 K3432 C3433 F3434 T3454

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Tue Nov 26 23:10:51 2024

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>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '6jii', asym_id = 'B', title = 'Modulation of cardiac ryanodine receptor 2 by calmodulin.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6jii', asym_id='B', title='Modulation of cardiac ryanodine receptor 2 by calmodulin.')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0005216,0005219,0005262,0005509,0006811,0006816,0006874,0016020,0055085,0070588', uniprot = '', pdbid = '6jii', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005216,0005219,0005262,0005509,0006811,0006816,0006874,0016020,0055085,0070588', uniprot='', pdbid='6jii', 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>