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BioLiP

Structure of PDB 6gdr Chain A Binding Site BS01

Receptor Information
>6gdr Chain A (length=256) Species: 314275 (Alteromonas mediterranea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVDGLQLAKQYGHQDINIAEYWVSEKLDGIRARWDGTELRTRNNNKIDAP
AWFTANWPKATIDGELWIARGQFERTASIVLSKLTLPSKRWAKVRFMAFD
MPVAGQSFDSRLNMLNNLKEATPNPTFAVVSQFTLSSVNALEEKLEQVTL
SGGEGLMLHHKKAFYHSGRSDKLIKVKQFEDAEAKVLAHFAGKGKFKGMM
GSLLVETPAGVQFKLGTGFSEKERRAPPAVGSWVTFKFYGVTKNGKPRFA
SFLRVR
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6gdr DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		K15 E82 S86 S90 K91 G202 R203 G226 K227 G228 K229 F230 G235 S236 K248 G250 T276 N278 F283
Binding residue
(residue number reindexed from 1)		K9 E74 S78 S82 K83 G168 R169 G192 K193 G194 K195 F196 G201 S202 K214 G216 T242 N244 F249
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Thu May 22 22:33:26 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 = '6gdr', asym_id = 'A', bs = 'BS01', title = 'DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6gdr', asym_id='A', bs='BS01', title='DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.')
   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 = '0003910,0005524,0006281,0006310', uniprot = '', pdbid = '6gdr', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003910,0005524,0006281,0006310', uniprot='', pdbid='6gdr', asym_id='A')
    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>