Structure of PDB 4c5n Chain B Binding Site BS01

Receptor Information
>4c5n Chain B (length=269) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWS
HDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQ
YFVVDPVMVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIED
MKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQS
YNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGP
VDHGAYNRIEHIDVEVTEV
Ligand information
Ligand IDPXL
InChIInChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3
InChIKeyRADKZDMFGJYCBB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)CO)C=O)O
ACDLabs 10.04O=Cc1c(cnc(c1O)C)CO
CACTVS 3.341Cc1ncc(CO)c(C=O)c1O
FormulaC8 H9 N O3
Name3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE;
PYRIDOXAL
ChEMBLCHEMBL102970
DrugBankDB00147
ZINCZINC000000120249
PDB chain4c5n Chain B Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4c5n A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G11 D13 G19 M80 H210 C214
Binding residue
(residue number reindexed from 1)		G11 D13 G19 M80 H203 C207
Annotation score1
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Feb 22 17:04:04 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>()
   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 = '4c5n', asym_id = 'B', bs = 'BS01', title = 'A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4c5n', asym_id='B', bs='BS01', title='A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.')
   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 = '0008972,0009228', uniprot = '', pdbid = '4c5n', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008972,0009228', uniprot='', pdbid='4c5n', 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>