Structure of PDB 4jkr Chain K Binding Site BS01

Receptor Information
>4jkr Chain K (length=90) Species: 536056 (Escherichia coli DH1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIAL
REIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR
Ligand information
Ligand IDG4P
InChIInChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyBUFLLCUFNHESEH-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H17 N5 O17 P4
NameGUANOSINE-5',3'-TETRAPHOSPHATE;
guanosine tetraphosphate;
ppGpp
ChEMBL
DrugBankDB04022
ZINCZINC000008217069
PDB chain4jkr Chain K Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jkr The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		A2 R3 V4
Binding residue
(residue number reindexed from 1)		A1 R2 V3
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sun Nov 17 14:53:35 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 = '4jkr', asym_id = 'K', bs = 'BS01', title = 'The mechanism of E. coli RNA polymerase regulati...p is suggested by the structure of their complex.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4jkr', asym_id='K', bs='BS01', title='The mechanism of E. coli RNA polymerase regulati...p is suggested by the structure of their complex.')
   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 = '0003677,0003899,0006351', uniprot = '', pdbid = '4jkr', asym_id = 'K'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003677,0003899,0006351', uniprot='', pdbid='4jkr', asym_id='K')
    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>