Structure of PDB 4rb4 Chain F Binding Site BS02

Receptor Information

>4rb4 Chain F (length=384) Species: 868200 (Escherichia coli DEC13E)

FITPPDTPTQAGPEYDFNDGARVLLPEGKWHVRLLDADSENILFCCDVDK
GWVTSSKKYFVRFRIQVFRQGEETPLLDETLKLKDRPVLISFPTGTLGAL
LGWFPYAERFQSLHKCRLECTMSQDIIDLLAPQYPQIQFSTPDKPRTVAP
YATYRVGLYFGGDTNNQPVDFRKVGFHRSAGYILGVDPREAPVRLDLSAP
RVIQEPYVCIATQSTCQAKYWNNGTGWSEVIAHLKSLGYRVMCIDRDAHY
GQGFVWNHIPWGAEDFTGKLPLQERVNLLRHASFFIGLPSGLSWLAWATR
IPVVLISGFSLPNSEFYTPWRVFNSHGCYGCWDDTSLNFDHHDFLWCPRH
KNTDRQFECTRLITGAQVNGVINKLHRSLTEQGV

Ligand information

• Ligand ID: AQH
• InChI: InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6-,8-,9-,10-,11-,12-,13+,16-,17-/m1/s1
• InChIKey: KMSFWBYFWSKGGR-GZNZTODLSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@@H]4[C@@H]([C@@H]([C@H]([C@@H](O4)[C@@H](CO)O)O)O)O)O)O)N
  ACDLabs 12.01: O=P(OP(=O)(OC1OC(C(O)C(O)C1O)C(O)CO)O)(OCC4OC(n2c3ncnc(N)c3nc2)C(O)C4O)O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@H](O)CO)[C@H](O)[C@@H](O)[C@H]4O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(CO)O)O)O)O)O)O)N
• Formula: C17 H27 N5 O16 P2
• Name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate
• ZINC: ZINC000263620659
• PDB chain: 4rb4 Chain F Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4rb4 A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family
• Resolution: 3.88 Å
• Binding residue (original residue number in PDB): T107 G109 A110 F187 Q224 T226 K230 R257 L283 R286 P300 S301 G302
• Binding residue (residue number reindexed from 1): T96 G98 A99 F176 Q213 T215 K219 R246 L272 R275 P289 S290 G291
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 21:25:46 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>()

   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 = '4rb4', asym_id = 'F', bs = 'BS02', title = 'A structural mechanism for bacterial autotranspo...ation by a dodecameric heptosyltransferase family'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4rb4', asym_id='F', bs='BS02', title='A structural mechanism for bacterial autotranspo...ation by a dodecameric heptosyltransferase family')

   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 = '0016757', uniprot = '', pdbid = '4rb4', asym_id = 'F'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016757', uniprot='', pdbid='4rb4', asym_id='F')

    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>