Structure of PDB 4yzv Chain YH

Receptor sequence

>4yzvYH (length=170) Species: 300852 (Thermus thermophilus HB8)

SRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVR
VERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGR
ALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAI
RKPSAYHEKGIYYAGEPVRL

3D structure

• PDB: 4yzv Defining the mRNA recognition signature of a bacterial toxin protein.
• Chain: YH
• Resolution: 3.1 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	YH	S2 R3 I4 R6 R59 K62 S63 L64 G66 L67 T70 N74 F109 S110 K138 Q139 G142 Q143 A146 Y157 H158 K160	S1 R2 I3 R5 R58 K61 S62 L63 G65 L66 T69 N73 F108 S109 K137 Q138 G141 Q142 A145 Y156 H157 K159
BS02	MG	YH	V79 S80	V78 S79

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 13:46:10 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 = '4yzv', asym_id = 'YH', title = 'Defining the mRNA recognition signature of a bacterial toxin protein.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4yzv', asym_id='YH', title='Defining the mRNA recognition signature of a bacterial toxin protein.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003735,0005840,0006412,0019843', uniprot = '', pdbid = '4yzv', asym_id = 'YH'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0019843', uniprot='', pdbid='4yzv', asym_id='YH')

    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>