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BioLiP

Structure of PDB 4c5n Chain D Binding Site BS01

Receptor Information

>4c5n Chain D (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
YFVVDPVMVCNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIED
MKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQS
YNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGP
VDHGAYNRIEHIDVEVTEV

Ligand information

Ligand ID

UEG

InChI

InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3

InChIKey

LXNHXLLTXMVWPM-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.9.2	Cc1c(c(c(cn1)CO)CO)O
ACDLabs 12.01	Oc1c(c(cnc1C)CO)CO
CACTVS 3.385	Cc1ncc(CO)c(CO)c1O

Formula

C8 H11 N O3

Name

4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol

PDB chain

4c5n Chain D Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	4c5n A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Resolution	1.75 Å
Binding residue (original residue number in PDB)	G11 G19 V42 V109 C110 C214
Binding residue (residue number reindexed from 1)	G11 G19 V42 V109 C110 C207
Annotation score	1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3
Tue May 20 03:26:20 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>()

1701 title=pdb2title(pdbid)

1702 if bs.startswith("BS"):

=> 1703 pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

1704 else:

1705 if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '4c5n', asym_id = 'D', 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='D', bs='BS01', title='A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.')

1326 display_ec(ec,csaOrig,csaRenu)

1327 if go:

=> 1328 display_go(go,uniprot,pdbid,asym_id)

1329 return pubmed,uniprot

1330

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

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

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>