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BioLiP

Structure of PDB 4c5n Chain C Binding Site BS02

Receptor Information

>4c5n Chain C (length=266) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSH
DVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQY
FVVDPVMNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKK
AATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNH
GAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDH
GAYNRIEHIDVEVTEV

Ligand information

Ligand ID

ACP

InChI

InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1

InChIKey

UFZTZBNSLXELAL-IOSLPCCCSA-N

SMILES

Software	SMILES
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O

Formula

C11 H18 N5 O12 P3

Name

PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE

PDB chain

4c5n Chain C Residue 500 [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)	K176 G178 K179 S186 D188 M203 F204 N209 H210 G211 A212 G213 C214 I245
Binding residue (residue number reindexed from 1)	K166 G168 K169 S176 D178 M193 F194 N199 H200 G201 A202 G203 C204 I235
Annotation score	3

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3
Sat May 17 20:14:00 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 = 'C', bs = 'BS02', 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='C', bs='BS02', 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 = '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>