Structure of PDB 6jiy Chain D

Receptor sequence

>6jiyD (length=3521) Species: 9823 (Sus scrofa)

QFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVPPD
LSICTFVLEQSLSVRALQEMLANGHRTLLYGHAILLRHSYSGMYLCCLST
SRSSTDKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSYLHVDAAFQQTLWSVAPISSAQGYLIGGDVLRLLHGECLT
VPSGEHEQRRTVHYEGGAVSVHARSLWRLETLRVAWSGSHIRWGQPFRLR
HVTTGKYLSLMEDKSLLLMDKEKADVKSTAFTFRSSKEKLKEVDGMGTSE
IKYGDSVCFIQHIGTGLWLTYQSSIQRKAIMHHEGHMDDGLNLSRSQHEE
SRTARVIRSTVFLFNRFIRGLDALSKKAKASTVDLPIESVSLSLQDLIGY
FHPPDEHLEHEDKQNRLRALKNRQNLFQEEGMINLVLECIDRLHVYSSVA
GREAGESWKSILNSLYELLAALIRGNRKNCAQFSGSLDWLISRLERLEAS
SGILEVLHCVLVESPEALNIIKEGHIKSIISLLDKHGRNHKVLDVLCSLC
VCHGVAVRSNQHLICDNLLPGRDLLLQTRLVNHVSSMRPNIFLGKKWYYE
LMVDHTEPFVTAEATHLRVGWASTEGYSPYPGGGEEWGGNGVGDDLFSYG
FDGLHLWSGCIARTVSSPNQHLLRTDDVISCCLDLSAPSISFRINGQPVQ
GMFENFNIDGLFFPVVSFSAGIKVRFLLGEFKFLPPPGYAPCYEAVLPKE
KLKVEHSREYKQERTYTRDLLGPTVSAFTPIPVDTSQIVLPPHLERIREK
LAENIHELWVMNKIELGWQYGPVRDDNKRQHPCLVEFSKLPEQERNYNLQ
MSLETLKTLLALGCHVGISDEHAYQLTSGYKPAPMDLSFIKLTPSQEAMV
DKLAENAHNVWARDRIRQRRNPRLVPYALLDDRTKKSNKDSLREAVRTLL
GYGYNLEARFRIFRAEKTYAVKAGRWYFEFEAVTAGDMRVGWSRPGCQPD
QELGSDERAFAFDGFKAQRWHQGNEHYGRSWQAGDVVGCMVDMTEHTMMF
TLNGEILLDDSGSELAFKDFDVGDGFIPVCSLGVAQVGRMNFGKDVSTLK
YFTICGLQEGYEPFAVNTNRDITMWLSKRLPQFLQVPSSHEHIEVTRIDV
TQKSFGSQNSSTDIMFYRLSMPIECTYYYSVRIFPNVWVGWITSDFHQYD
TAFDLVTVTLGDEKGKVHESIKRSNYMVCANNGLEIGCVVGLLTFTANGK
DLSTYYQVEPSTKLFPAVFAQATSPNVFQFEAGLFKSEHKNPVPQCPPRL
HVQFLSHVLWSRMPNQFLKVDVSRISERQGWLVQCLEPLQFMSLHIPEEN
RSVDILELTEQEELLKFHYHTLRLYSAVCALGNHRVAHALCSHVDEPQLL
YAIENKYMPGLLRAGYYDLLIDIHLSSYATARLMMNNEFIVPMTEETKSI
TLFPDGLPGIGLSTSLRPRMQFSSPSFVSINNECYQYSPEFPLDILKAKT
IQMLTEAVQEGSLHARDPVGGTTEFLFVPLIKLFYTLLIMGIFHNEDLKH
ILQLIEPSGLLQMKLPEPVKLQMCLLLQYLCDCQVRHRIEAIVAFSDDFV
AKLQDNQRFRYNEVMQALNCPCPEEIRDQLLDFHEDLMTHCGIELDLTIR
GRLLSLVEKVTYTLQQLISETMVRWAQESVIEDPELVRAMFVLLHRQYDG
IGGLVRALPKTYTINGVSVEDTINLLASLGQIRSLLSVEEEKLMIRGLGD
IMNNKVFYQHPNLMRALGMHETVMEVMVNVLGPKMVANCCRFLCYFCRIS
RQNQKAMFDHLSYLLENSSVGLASPAMRGSTPLDVAAASVMDNNELALAL
REPDLEKVVRYLAGCGLPVEGERYLDFLRFAVFCNGESVEENANVVVRLL
IRRPEGLLAAMEEAIKIAEGNAIMTFYAALIDLLGRCAPEMHLIHAAKGE
AIRIRSILRSLIPLGDLVGVISIAFQFCPDHKAAMVLFLDRVYVQDFLLH
LLEVGFLPDLRAAASLTDMALALNRYLCTAVLPLLFAGTEHHASLIDSLL
HTVKGCSLTKAQRDSIEVCLLSRPSMMQHLLRRLVFDVPLLNKMPLKLLT
NHYERCWKYYCLPGGASEEELHLSRKLFWGIFDALYEQELFKLALPCLSA
VAGALPPNFNPQPVDTSNITIPEKLEYFINKYAEHSHDKWSMDKLANGWI
YGEIYSDSSKVQPLMKPYKLLSEKEKEIYRWPIKESLKTMLAWGWRIERT
REGDAAHGYSPRAIDMSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELES
KGGGNHPLLVPYDTLTAKEKAKDREKAQDILKFLQINGYAVSRGYFLSAA
SRPLCSGGHASNKEKEMVFCKLGVLVRHRISLFGNDATLHILGQTLDART
VMKTGLESVKFLDNAAEDLEKTMENLKQGQFTTTVALLPMLSSLFEHIGQ
HQFLEDVQVSCYRILTSLYALGQRSALGECLAAFAGAAFLETHLDKHNIY
SKAVWHKLLSKQRKRAVVACFRMAPLYNLPRHRAVNLFLQGYEKSWIETE
EHYFEDKLIEDLAKPRVDPLHQLILLFSRTALTEKCKLEEDFLYMAYADI
MAKSCSFEEKEMEKQKLLYQQARLHDRGAAEMVLQTISASKGETGPMVAA
TLKLGIAILNGGNSTVQQKMLEYLKEKKDVGFFQSLAGLMQSCSVLDLNA
FERQNKAEGLGMVTEEGSGEKVLQDDEFTCDLFRFLQLLCEGHNSDFQNY
LRTQTGNNTTVNIIISTVDYLLRVQESISDFYWYYSGKDVIDEQGQRNFS
KAIQVAKQVFNTLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMQMK
LSQDSSQIELLKELMDLQKDMVVMLLSMLEGNVVNGTIGKQMVDMLVESS
NNVEMILKFFDMFLKLKDLTSSDTFKEYDPDGKGVISKRDFHKAMESHKH
YTQSETEFLLSCAETDENETLDYEEFVKRFHEPAKDIGFNVAVLLTNLSE
HMPNDTRLQTFLELAESVLNYFQPFLGRIEIMGSAKRIERVYFEISESSR
TQWEKPQVKESKRQFIFDVVNEGGEKEKMELFVNFCEDTIFEMQLAAQII
AYQQKLLNYFARNFYNMRMLALFVAFAINFILLFYKVVHYVLEESSGYME
PTLRILAILHTVISFFCIIGYYCLKVPLVIFKREKEVARKLEFDGLYITE
QPSEDDIKGQWDRLVINTQSFPNNYWDKFVKRKVMDKYGEFYGRDRISEL
LGSAVLNSIDVKYQMWKLGVVFTDNSFLYLAWYMTMSVLGHYNNFFFAAH
LLDIAMGFKTLRTILSSVTHNGKQLVLTVGLLAVVVYLYTVVAFNFFRKF
YNKSEDGDTPDMKCDDMLTCYMFHMYVGVRAGGGIGDEIEDPAGDEYEIY
RIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICG
IGNDYFDTVPHGFETHTLQEHNLANYLFFLMYLINKDETEHTGQESYVWK
MYQERCWEFFPAGDCFRKQYE

3D structure

• PDB: 6jiy Modulation of cardiac ryanodine receptor 2 by calmodulin.
• Chain: D
• Resolution: 3.9 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	C4889 C4892 H4909	C3446 C3449 H3466
BS02	CA	D	E3849 E3923 T4932	E2741 E2815 T3489
BS03	ATP	D	K4170 R4171 F4890 T4910 L4916	K3062 R3063 F3447 T3467 L3473
BS04	CFF	D	W4646 I4927 Y4945	W3226 I3484 Y3502

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Dec 2 03:19:53 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 = '6jiy', asym_id = 'D', title = 'Modulation of cardiac ryanodine receptor 2 by calmodulin.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6jiy', 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 = '6jiy', 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='6jiy', 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>