Structure of PDB 5goa Chain B Binding Site BS01

Receptor Information

>5goa Chain B (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

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5goa Chain B Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5goa Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2
• Resolution: 4.2 Å
• Binding residue (original residue number in PDB): C4889 C4892 H4914
• Binding residue (residue number reindexed from 1): C3348 C3351 H3373
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Nov 25 20:10:20 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>()

   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 = '5goa', asym_id = 'B', bs = 'BS01', title = 'Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5goa', asym_id='B', bs='BS01', title='Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2')

   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 = '0005216,0005219,0005262,0005509,0006811,0006816,0006874,0016020,0055085,0070588', 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>