Structure of PDB 5xxb Chain O

Receptor sequence

>5xxbO (length=158) Species: 5811 (Toxoplasma gondii)

VKYAKESNENKCCKAFGQDLRVHFKNTHATVQAIKKDKKGNPMKLSAAKK
FLEDVMEKKRCVPFRKFTGCIGRKAQAKEFKHTQGRWPVKSCKFVLDLLR
NAESNAEMKNLDVDNLVIEHIQVNRAPKGRRRTYRAHGRINPYMSQPCHI
EVILREQE

3D structure

• PDB: 5xxb Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
• Chain: O
• Resolution: 3.17 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	rna	O	V2 Y4 K16 F18 Q20 R23 H25 F26 K27 H30 K37 K40 K68 F69 G71 C72 G74 R75 K76 A77 Q78 K80 E81 Q86 R88 W89 P90 K92 N103 S106 N107 Q124 V125 K130 R133 Y136 R137 A138 H139 G140 I142 N143 P144 Y145 M146	V1 Y3 K14 F16 Q18 R21 H23 F24 K25 H28 K35 K38 K66 F67 G69 C70 G72 R73 K74 A75 Q76 K78 E79 Q84 R86 W87 P88 K90 N101 S104 N105 Q122 V123 K128 R131 Y134 R135 A136 H137 G138 I140 N141 P142 Y143 M144
BS02	rna	O	A5 R67 N126 R127 P129 H151	A4 R65 N124 R125 P127 H149

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 01:57:34 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 = '5xxb', asym_id = 'O', title = 'Cryo-EM structures of the 80S ribosomes from hum...sites Trichomonas vaginalis and Toxoplasma gondii'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='5xxb', asym_id='O', title='Cryo-EM structures of the 80S ribosomes from hum...sites Trichomonas vaginalis and Toxoplasma gondii')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003735,0005840,0006412,0015934', uniprot = '', pdbid = '5xxb', asym_id = 'O'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0015934', uniprot='', pdbid='5xxb', asym_id='O')

    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>