Structure of PDB 7jil Chain f Binding Site BS01

Receptor Information

>7jil Chain f (length=38) Species: 986 (Flavobacterium johnsoniae)

MKVRASVKKRSAECIIVRRKGRLYVINKKNPRFKQRQG

Ligand information

>7jil Chain 1 (length=2742)

aaauaagggcguauggggaaugccuaggcucucagaggcgaugaaggacg
ugauaagcugcgaaaagcugcggggacuggcacacacagauugauccgca
gauauccgaauggggcaacccgcuauauugaagauauagcacaccgauag
gugggcaaacccgcugaacugaaacaucuaaguaggcggaggagaagaaa
acaaaagugauuccguaaguaguggcgagcgaacgcggauuagcccaaac
cagugcuacggcagugcugggguuguaacaugcagaaccggaaguuacug
gaaagugacgccaaagagggugauagccccguauggguaauaaauguggu
auccugaguagggcgggacacgugaaacccugucugaauucggcgggacc
auccgcuaaggcuaaauacuccugagagaccgauagugaaccaguaccgu
gagggaaaggugaaaagaaccgugaauaacggagugaaauagauccugaa
accauacgcuuacaagcggucggagcccuuucguggggugacggcgugcc
uuuugcauaaugagccuacgaguuaacgcugcuggcaaggauaaguacuu
caguacggauccgcagcgaaagcgagucugaauagggcgcuuuagucagu
aguguuagacgcgaaaccgugugaucuacccaugggcagguugaagcugu
gguaacacacaguggaggaccgaaccgguugacguugaaaagucuucgga
ugaccuguggguaggggugaaaggccaaucaaacucggaaauagcucgua
cuccccgaaaugcauuuaggugcagcguuaguuauaaaguuauacagagg
uagagcuacugauuggaugcgggggcuucaccgcccaccaauuccugaca
aacuccgaaugcuguauaauguucacuaacagugagggcuugggugcuaa
gguccaaguccgagagggaaagaacccagaccaucagcuaagguccccaa
auauaugcuaaguugaaagaacgagguuugucugcccagacagcuaggau
guuggcuuggaagcagcccauuuaaagagcguaacagcucacuagucgag
cggacgagcauggauaauaaucgggcauaagcauauuaccgaagcuaugg
auuugcaaguuugcaagugguaggggagcauucuaacaggguugaagguu
uuucguaaggagggcuggacugguuagaaaagaaaauguaggcauaagua
acgauaaugcgggcgagaaacccgcacaccgaaaaacuaagguuuccaca
gcuaugcuaaucagcuguggguuagucugguccuaaggcgaacccgaaag
ggacagucgauggcuaacggguuaauauucccguacuacuaauuacugug
auggggugacggagugaugaaagcgccgcgaacugacggaauaguucguu
gaaguaccuagcuauagguccuguaguaaaaugcgcaggaacuggugaaa
uacgauaguacucggagucgacaaagagauagugcgccuaagggcuucca
agaaaaaccucuaaacuucagguaauuaguaccaguaccguaaaccgaca
cagguaguugaggagagaauccuaaggugcucgagauauucauggcuaag
gaauuaggcaaaauagaccuguaacuucgggagaaaggucgcccugagca
aucagggccgcagugaagagguccaggcgacuguuuaucaaaaacacagg
gcucugcaaaaucguaagaugaaguauagggccugacaccugcccggugc
uggaagguuaagaggagauguuaucuucggagaagcauugaauugaagcc
ccaguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaaugguguaacgaucuggacacugu
cucagccaugagcucggugaaauuguaguaacggugaagaugccguuuac
ccgcagugggacgaaaagacccugugcaccuuuacuauagcuuaguacug
accuuggauaaauguuuaucugaggccuaaccucgcugcgggggacagug
cuugguggguaguuugacugggguggucgccuccaaaagaguaacggagg
cuucuaaagguucccucaguacgcuugguaaccgugcguagagugcaaug
gcauaagggagcuugacugagagacauacaggucgaucagguacgaaagu
agagcauagugauccggugguuccgcauggaagggccaucgcucaaagga
uaaaagguacgccggggauaacaggcugaucucccccaagaguucauauc
gacggggggguuuggcaccucgaugucggcucgucacauccuggggcugg
agaaggucccaaggguugggcuguucgcccauuaaagugguacgcgagcu
ggguucagaacgucgugagacaguucggucucuaucuacugcgggcguua
gaaauuugaguggaucugauucuaguacgagaggaccgaauuggacuaac
cucuaguguaucuguugucccgccaggggcaccgcagaguagcuacguug
ggaagggauaagcgcugaaagcauauaagcgcgaaacccaccacaagaug
agauuucuuuuaaggaucguggaagaugaccacguugauaggcuauagau
guaaaggcaguaaugucauagucgaguaguacuaauaauccg

......<<<<<<<<<<.....<<<..<<<<<<<<<<<<<......<<<<<
<.....((.>>>.....<<<<<<<..<<<)).....>>>.....>>>>>>
>...>>>....<<<....>>><<<<<<<.....>>>>>>>.<<<<....>
>>>.>>...<<<<<<.....<<....>>......>>>>>.>.........
<<....>>...<<<<<.....<<.....>>....>>>>>...<<<....<
<<<<<<<.....>>>>>>>>.......<.<<......<<<...<<<<<..
....>>>>>((......<<<.....))>>>...>>>.......>>.....
.>........<<<<<<<...........>>>>>>>......<<<<<..<<
<<>>>>>..>>>......>>.>>>>>>>.>>...............<<..
..>>....>>.........<<<<.....>>>>.............>....
.>>>>>>>>>>.......<<<<..<<<<<.....>>>>>..>>>>...<.
<........>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<<.<.
..>>>>...>>>...<<....>>..<<<<.....>>>>......>>>>>>
>>>>>>>..<<.<...<<<.<<.....<<<<<<<<<..<<<....<<<<<
<......>>>>>>.....>>>...<<<...<<<........>>>..>>>.
...>>>>>>>>>...<<<.....>>>......>>.>>>......>.>>..
<<<<<<....<<<<<....>>>>><<<<<<<<......<<<<<<<<<...
..<<<....<<.<.<<<....<<<<.........>>.>>...>>>.>.>>
..>>.>.....>>>>>>>>>....>>>>>>.>>..<<<<<<<<<<.....
.>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((...
..<<<<<<.....<<......<<..<<<<<<<<<<.......<<<<<.<<
<..<<<<.......>>>>>>>.......<<......>>...>>>>>...>
>>>>>>>>>.>>..........)))>>...>>>>>>.>>>...>>>>>>>
<<<<<<<<..>>>>>>>>....>>>>>>..<<<<<<<.<.......<<<<
<<<<....>>>>>>>>....>.>>>>>>>........>>>>>><......
<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<
<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>
>>...>>>...>>...<<<<<........>>>>>))<<<<<<<<<<<<<.
..<<<<<...<<<<<.......<<<<.<<<<<<....[[....>>>>>>.
...<<<....<<<..<<.<<<<<<.<<.....>>>>>>>>.>>>>>....
>>>.......<<<...<<..>>...>>>.....>>>>......>>>>>..
......>>>>>...>>....>>>>>>>>>>>>>>>..>>.....<<....
..>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<
.........<.....<<<<<....<<..>>.....>>>>><<<<<<<...
.>>>>>>>............<<<<<<<<<..<<<.........>>>..<<
<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<
<<<..<<<<..<<...<<<<<<.<<....>>..>>>>>>...>>..>>>>
>>>>>..>>>>><<<<<<.......>>>>>>........<..........
.<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..
>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<
<<<<<<<.<<<.<<......<<<<.<<<<<<..<<<<<.<<<.<<<<<.<
.<<<<<<<<<<<..>>>>>>>>>>>.>...<<<<<<.>>>>>>....>>>
>>.>>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>
>..<<...<<<<<<<...<<<<<.........>>>>>.....<<...(((
>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>
>.>>))).......<<<<<<<.<<..>>>>..>>>>>>>>>.........
....>>>>..>>>>>>.......<<<<.<.<<<<<<...<<.......>>
...>>>>>>...>>>>.>.......<<<<<.<.<<<<..<<<<<<<<<..
....>>>>>>..>>>.<<<<<.....>>>>>.....>>>>...>...>>>
.>>....<<<<<<<....>>>.>>>>....>>..>>>>>>>>>>>....<
<<<<<<...<<<<..<<<<<<<...............>>>>>>>.<<<<<
...<<<<...<<<<<<<<<<<.]].>>>>>>..>>>>>...>>>>.>>>>
>...<<<....<<<<<...........>>>>>....>>>.>>>>......
.>>>>>>>.....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<
.....<<<<....>>>>...>>>..>>>>>.>>>...>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7jil Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): M1 R4 A5 S6 V7 K8 R10 R18 R19 K20 R22 L23 Y24 P31 R32 K34 R36 Q37 G38
• Binding residue (residue number reindexed from 1): M1 R4 A5 S6 V7 K8 R10 R18 R19 K20 R22 L23 Y24 P31 R32 K34 R36 Q37 G38

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 15:57:16 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 = '7jil', asym_id = 'f', bs = 'BS01', title = 'Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7jil', asym_id='f', bs='BS01', title='Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.')

   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 = '0003735,0005840,0006412', uniprot = '', pdbid = '7jil', asym_id = 'f'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='7jil', asym_id='f')

    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>