Structure of PDB 5goa Chain B

Receptor sequence

>5goaB (length=3423) 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
DGLPGIGLSTSLRPRMQFSSPSFVSYSPEFPLDILKAKTIQMLTEAVQEG
SLHARDPVGGTTEFLFVPLIKLFYTLLIMGIFHNEDLKHILQLIEPSGLL
QMKLPEPVKLQMCLLLQYLCDCQVRHRIEAIVAFSDDFVAKLQDNQRFRD
FHEDLMTHCGIELDLTIRGRLLSLVEKVTYTLQQLISETMVRWAQESVIE
DPELVRAMFVLLHRQYDGIGGLVRALPKTYTINGVSVEDTINLLASLGQI
RSLLSVEEEKLMIRGLGDIMNNKVFYQHPNLMRALGMHETVMEVMVNVLG
PKMVANCCRFLCYFCRISRQNQKAMFDHLSYLLENSSVTPLDVAAASVMD
NNELALALREPDLEKVVRYLAGCGLPVEGERYLDFLRFAVFCNGESVEEN
ANVVVRLLIRRPEGLLAAMEEAIKIGNAIMTFYAALIDLLGRCAEAIRIR
SILRSLGDLVGVISIAFQFCPDHKAAMVLFLDRVYVQDFLLHLLGFLPDL
RAAASLTDMALALNRYLCTAVLPLLPLFAGTEHHASLIDSLLHTVKGCSL
TKAQRDSIEVCLLSRPSMMQHLLRRLVFDVPLLNKMPLKLLTNHYERCWK
YYCLPGGASEEELHLSRKLFWGIFDALYEQELFKLALPCLSAVAGALPPN
FNPQPVDTSNITIPEKLEYFINKYAEHSHDKWSMDKLANGWIYGEIYSDS
SKVQPLMKPYKLLSEKEKEIYRWPIKESLKTMLAWGWRIERTREGDVDAA
HGYSPRAIDMSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELESKGGGNH
PLLVPYDTLTAKEKAKDREKAQDILKFLQINGYAVSRGYFLSAASRPLCS
GGHASNKEKEMVFCKLGVLVRHRISLFGNDATLHILGQTLDARTVMKTGL
ESVKFLDNAAEDLEKTMENLKQGQFTTTVALLPMLSSLFEHIGQHQFLED
VQVSCYRILTSLYALGTSVERQRSALGECLAAFAGAAFLETHLDKHNIYS
PRHRAVNLFLQGYEKSWIETEEHYFEDKLIEDLAKPRVDPLHQLILLFSR
TALTEKCKLEEDFLYMAYADIMAKSCSFEEKEMEKQKLLYQQARLHDRGA
AEMVLQTISASKGETGPMVAATLKLGIAILNGGNSTVQQKMLEYLKEKKD
VGFFQSLAGLMQSCSVLDLNAFERQNKDDEFTCDLFRFLQLLCEGHNSDF
QNYLRTQTGNNTTVNIIISTVDYLLRVQESISDFYWYYSGKDVIDEQGQR
NFSKAIQVAKQVFNTLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHM
QMKLSQDSSQIELLKELMDLQKDMVVMLLSMLEGNVVNGTIGKQMVDMLV
ESSNNVEMILKFFDMFLKLKDLTSSDTFKEYDPDGKGVISKRDFHKAMES
HKHYTQSETEFLLSCAETDENETLDYEEFVKREPAKDIGFNVAVLLTNLS
EHMPNDTRLQTFLELAESVLNYFQPFLGRIEIMGSAKRIERVYFEISESS
RTQWEKPQVKESKRQFIFDVVNEGGEKEKMELFVNFCEDTIFEMQLAAQI
IAYQQKLLNYFARNFYNMRMLALFVAFAINFILLFYKVSVHYVLEESSGY
MEPTLRILAILHTVISFFCIIGYYCLKVPLVIFKREKEVARKLEFDGLYI
TEQPSEDDIKGQWDRLVINTQSFPNNYWDKFVKRKVMDKYGEFYGRDRIS
ELLGSAVLNSIDVKYQMWKLGVVFTDNSFLYLAWYMTMSVLGHYNNFFFA
AHLLDIAMGFKTLRTILSSVTHNGKQLVLTVGLLAVVVYLYTVVAFNFFR
KFYNKSEDGDTPDMKCDDMLTCYMFHMYVGVRAGGGIGDEIEDPAGDEYE
IYRIIFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFI
CGIGNDYFDTVPHGFETHTLQEHNLANYLFFLMYLINKDETEHTGQESYV
WKMYQERCWEFFPAGDCFRKQYE

3D structure

• PDB: 5goa Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2
• 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	C3348 C3351 H3373

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Nov 25 22:31:30 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 = '5goa', asym_id = 'B', title = 'Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='5goa', asym_id='B', title='Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2')

    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 = '5goa', 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='5goa', 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>