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Structure of PDB 4c5n Chain C

Receptor sequence

>4c5nC (length=266) Species: 1280 (Staphylococcus aureus)

ALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSH
DVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQY
FVVDPVMNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKK
AATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNH
GAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDH
GAYNRIEHIDVEVTEV

3D structure

• PDB: 4c5n A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
• Chain: C
• Resolution: 1.75 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	PXL	C	G11 G19 C214	G10 G18 C204
BS02	ACP	C	K176 G178 K179 S186 D188 M203 F204 N209 H210 G211 A212 G213 C214 I245	K166 G168 K169 S176 D178 M193 F194 N199 H200 G201 A202 G203 C204 I235

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun May 18 00:58:06 2025

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>()

   1709                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1710         else:

=> 1711             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1712     

   1713     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '4c5n', asym_id = 'C', title = 'A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4c5n', asym_id='C', title='A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.')

    843 

    844     if go:

=>  845         display_go(go,uniprot,pdbid,asym_id)

    846     return pubmed,uniprot

    847 

global display_go = <function display_go>, go = '0008972,0009228', uniprot = '', pdbid = '4c5n', asym_id = 'C'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008972,0009228', uniprot='', pdbid='4c5n', asym_id='C')

    484         '''.replace("$namespace_link",namespace_link

    485           ).replace("$namespace",namespace

=>  486           ).replace("$uniprot",u

    487         ))

    488         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>