Structure of PDB 6gdr Chain A Binding Site BS03

Receptor Information

>6gdr Chain A (length=256) Species: 314275 (Alteromonas mediterranea)

IVDGLQLAKQYGHQDINIAEYWVSEKLDGIRARWDGTELRTRNNNKIDAP
AWFTANWPKATIDGELWIARGQFERTASIVLSKLTLPSKRWAKVRFMAFD
MPVAGQSFDSRLNMLNNLKEATPNPTFAVVSQFTLSSVNALEEKLEQVTL
SGGEGLMLHHKKAFYHSGRSDKLIKVKQFEDAEAKVLAHFAGKGKFKGMM
GSLLVETPAGVQFKLGTGFSEKERRAPPAVGSWVTFKFYGVTKNGKPRFA
SFLRVR

Ligand information

>6gdr Chain D (length=11)

cactatcggaa

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gdr DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.
• Resolution: 2.33 Å
• Binding residue (original residue number in PDB): R50 T251 F253 S254 E255 K271 F283 S285
• Binding residue (residue number reindexed from 1): R42 T217 F219 S220 E221 K237 F249 S251

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Dec 1 19:21:46 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 = '6gdr', asym_id = 'A', bs = 'BS03', 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='BS03', title='DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.')

   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 = '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')

    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>