Structure of PDB 6gdr Chain A Binding Site BS01

Receptor Information

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

IVDGLQLAKQYGHQDINIAEYWVSEKLDGIRARWDGTELRTRNNNKIDAP
AWFTANWPKATIDGELWIARGQFERTASIVLSKLTLPSKRWAKVRFMAFD
MPVAGQSFDSRLNMLNNLKEATPNPTFAVVSQFTLSSVNALEEKLEQVTL
SGGEGLMLHHKKAFYHSGRSDKLIKVKQFEDAEAKVLAHFAGKGKFKGMM
GSLLVETPAGVQFKLGTGFSEKERRAPPAVGSWVTFKFYGVTKNGKPRFA
SFLRVR

Ligand information

>6gdr Chain B (length=21)

ttccgatagtggggtcgcaat

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): 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

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Dec 1 20:01:25 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 = '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.')

   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>