Structure of PDB 6jiu Chain D

Receptor sequence

>6jiuD (length=3496) Species: 9823 (Sus scrofa)

QFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVPPD
LSICTFVLEQSLSVRALQEMLANGHRTLLYGHAILLRHSYSGMYLCCLST
SRKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILVSVSSE
RYLHLSYLHVDAAFQQTLWSVAPISSAQGYLIGGDVLRLLHGECLTVPSG
EHEQRRTVHYEGGAVSVHARSLWRLETLRVAWSGSHIRWGQPFRLRHVTT
GKYLSLMEDKSLLLMDKEKADVKSTAFTFRSSKEKLRKEVDGMGTSEIKY
GDSVCFIQHIGTGLWLTYQSSIQRKAIMHHEGHMDDGLNLSRSQHEESRT
ARVIRSTVFLFNRFIRGLDALSKKAKASTVDLPIESVSLSLQDLIGYFHP
PDEHLEHEDKQNRLRALKNRQNLFQEEGMINLVLECIDRLHVYSSVAGRE
AGESWKSILNSLYELLAALIRGNRKNCAQFSGSLDWLISRLERLEASSGI
LEVLHCVLVESPEALNIIKEGHIKSIISLLDKHGRNHKVLDVLCSLCVCH
GVAVRSNQHLICDNLLPGRDLLLQTRLVNHVSSMRPNIFLGKKWYYELMV
DHTEPFVTAEATHLRVGWASTEGYSPYPGGGEEWGGNGVGDDLFSYGFDG
LHLWSGCIARTVSSPNQHLLRTDDVISCCLDLSAPSISFRINGQPVQGMF
ENFNIDGLFFPVVSFSAGIKVRFLLGEFKFLPPPGYAPCYEAVLPKEKLK
VEHSREYKQERTYTRDLLGPTVSAFTPIPVDTSQIVLPPHLERIREKLAE
NIHELWVMNKIELGWQYGPVRDDNKRQHPCLVEFSKLPEQERNYNLQMSL
ETLKTLLALGCHVGISDEHAYQLTSGYKPAPMDLSFIKLTPSQEAMVDKL
AENAHNVWARDRIRQRRNPRLVPYALLDDRTKKSNKDSLREAVRTLLGYG
YNLEARFRIFRAEKTYAVKAGRWYFEFEAVTAGDMRVGWSRPGCQPDQEL
GSDERAFAFDGFKAQRWHQGNEHYGRSWQAGDVVGCMVDMTEHTMMFTLN
GEILLDDSGSELAFKDFDVGDGFIPVCSLGVAQVGRMNFGKDVSTLKYFT
ICGLQEGYEPFAVNTNRDITMWLSKRLPQFLQVPSSHEHIEVTRIDVTQK
SFGSQNSSTDIMFYRLSMPIECTYYYSVRIFPNVWVGWITSDFHQYDTAF
DLVTVTLGDEKGKVHESIKRSNYMVCANNGLEIGCVVGLLTFTANGKDLS
TYYQVEPSTKLFPAVFAQATSPNVFQFEAGLFKSEHKNPVPQCPPRLHVQ
FLSHVLWSRMPNQFLKVDVSRISERQGWLVQCLEPLQFMSLHIPEENRSV
DILELTEQEELLKFHYHTLRLYSAVCALGNHRVAHALCSHVDEPQLLYAI
ENKYMPGLLRAGYYDLLIDIHLSSYATARLMMNNEFIVPMTEETKSITLF
PDGLPGIGLSTSLRPRMQFSSPSFVSINNECYQYSPEFPLDILKAKTIQM
LTEAVQEGSLHARDPVGGTTEFLFVPLIKLFYTLLIMGIFHNEDLKHILQ
LIEPSGLLQMKLPEPVKLQMCLLLQYLCDCQVRHRIEAIVAFSDDFVAKL
QDNQRFRYNEVMQALNCPCPEEIRDQLLDFHEDLMTHCGIELDLTIRGRL
LSLVEKVTYTLQQLISETMVRWAQESVIEDPELVRAMFVLLHRQYDGIGG
LVRALPKTYTINGVSVEDTINLLASLGQIRSLLSVEEEKLMIRGLGDIMN
NKVFYQHPNLMRALGMHETVMEVMVNVLGPKMVANCCRFLCYFCRISRQN
QKAMFDHLSYLLENSSVTPLDVAAASVMDNNELALALREPDLEKVVRYLA
GCGLPVEGERYLDFLRFAVFCNGESVEENANVVVRLLIRRPEGLLAAMEE
AIKIGNAIMTFYAALIDLLGRCAPEMHLIHAAKGEAIRIRSILRSLIPLG
DLVGVISIAFQFCPDHKAAMVLFLDRVYVQDFLLHLLEVGFLPDLRAAAS
LTDMALALNRYLCTAVLPLLLFAGTEHHASLIDSLLHTVKGCSLTKAQRD
SIEVCLLSPSMMQHLLRRLVFDVPLLNKMPLKLLTNHYERCWKYYCLPGG
ASEEELHLSRKLFWGIFDALYEQELFKLALPCLSAVAGALPPNFNPQPVD
TSNITIPEKLEYFINKYAEHSHDKWSMDKLANGWIYGEIYSDSSKVQPLM
KPYKLLSEKEKEIYRWPIKESLKTMLAWGWRIERTREGDAAHGYSPRAID
MSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELESKGGGNHPLLVPYDTL
TAKEKAKDREKAQDILKFLQINGYAVSRGYFLSAASRPLCSGGHASNKEK
EMVFCKLGVLVRHRISLFGNDATLHILGQTLDARTVMKTGLESVKFLDNA
AEDLEKTMENLKQGQFTTTVALLPMLSSLFEHIGQHQFLEDVQVSCYRIL
TSLYALGTSVERQRSALGECLAAFAGAAFLETHLDKHNIYSLLSKQRKRA
VVACFRMAPLYNLPRHRAVNLFLQGYEKSWIETEEHYFEDKLIEDLAKPR
VDPLHQLILLFSRTALTEKCKLEEDFLYMAYADIMAKSCSFEEKEMEKQK
LLYQQARLHDRGAAEMVLQTISASKGETGPMVAATLKLGIAILNGGNSTV
QQKMLEYLKEKKDVGFFQSLAGLMQSCSVLDLNAFERQNKAEGLGGSGEK
VLQDDEFTCDLFRFLQLLCEGHNSDFQNYLRTQTGNNTTVNIIISTVDYL
LRVQESISDFYWYYSGKDVIDEQGQRNFSKAIQVAKQVFNTLTEYIQGPC
TGNQQSLAHSRLWDAVVGFLHVFAHMQMKLSQDSSQIELLKELMDLQKDM
VVMLLSMLEGNVVNGTIGKQMVDMLVESSNNVEMILKFFDMFLKLKDLTS
SDTFKEYDPDGKGVISKRDFHKAMESHKHYTQSETEFLLSCAETDENETL
DYEEFVKRFHEPAKDIGFNVAVLLTNLSEHMPNDTRLQTFLELAESVLNY
FQPFLGRIEIMGSAKRIERVYFEISESSRTQWEKPQVKESKRQFIFDVVN
EGGEKEKMELFVNFCEDTIFEMQLAAQIIAYQQKLLNYFARNFYNMRMLA
LFVAFAINFILLFYKVVHYVLEESSGYMEPTLRILAILHTVISFFCIIGY
YCLKVPLVIFKREKEVARKLEFDGLYITEQPSEDDIKGQWDRLVINTQSF
PNNYWDKFVKRKVMDKYGEFYGRDRISELLGNSIDVKYQMWKLGVVFTDN
SFLYLAWYMTMSVLGHYNNFFFAAHLLDIAMGFKTLRTILSSVTHNGKQL
VLTVGLLAVVVYLYTVVAFNFFRKFYNKSEDGDTPDMKCDDMLTCYMFHM
YVGVRAGGGIGDEIEDPAGDEYEIYRIIFDITFFFFVIVILLAIIQGLII
DAFGELRDQQEQVKEDMETKCFICGIGNDYFDTVPHGFETHTLQEHNLAN
YLFFLMYLINKDETEHTGQESYVWKMYQERCWEFFPAGDCFRKQYE

3D structure

• PDB: 6jiu Modulation of cardiac ryanodine receptor 2 by calmodulin.
• Chain: D
• 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	D	I4891 C4892 H4914	I3423 C3424 H3446
BS02	CA	D	E3849 E3923 T4932	E2720 E2794 T3464
BS03	ATP	D	K4170 R4171 M4885 F4890 T4910	K3041 R3042 M3417 F3422 T3442
BS04	CFF	D	W4646 I4927 Y4945	W3205 I3459 Y3477

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 22 22:48:48 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 = '6jiu', asym_id = 'D', title = 'Modulation of cardiac ryanodine receptor 2 by calmodulin.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6jiu', asym_id='D', 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 = '6jiu', asym_id = 'D'

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

    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>