Structure of PDB 3rfc Chain A Binding Site BS01

Receptor Information
>3rfc Chain A (length=344) Species: 342109 (Xanthomonas oryzae pv. oryzae MAFF 311018) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHV
NDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQQALAQIDVVF
PIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARL
AVAPFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADA
FAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVVEIVI
PADIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLP
GFTRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3rfc Chain A Residue 368 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3rfc Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP
Resolution2.1 Å
Binding residue
(original residue number in PDB)
F183 K185 S192 A223 V224 E228 F304
Binding residue
(residue number reindexed from 1)
F180 K182 S189 A220 V221 E225 F284
Annotation score5
Gene Ontology
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UnboundLocalError
Python 3.6.8: /usr/bin/python3
Sun Nov 24 03:46:41 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 = '3rfc', asym_id = 'A', bs = 'BS01', title = 'Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3rfc', asym_id='A', bs='BS01', title='Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP')
   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 = '0005524,0005737,0008716,0046872', uniprot = '', pdbid = '3rfc', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005524,0005737,0008716,0046872', uniprot='', pdbid='3rfc', asym_id='A')
    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>