Structure of PDB 6q97 Chain S Binding Site BS01

Receptor Information
>6q97 Chain S (length=108) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLE
SAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSH
ITVVVSDR
Ligand information
>6q97 Chain 1 (length=2903) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaacccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugauguguaggauaggugggaggcuuugaaguguggacgccaguc
ugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu
<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<.<<<....(((.>>>.....<<<<<<<..<<.))).....>>...
...>>>>>>>....>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<...........>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>...<<<<<.....<<....
.>>....>>>>>...(((.....<.......<...<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>...>....>...........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<......>....]].........<<.........>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<.....<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<.<.....>.>>
.....>>>>>>>>>>>>...<<.<...<<<<<<.....<<<<<<<<...<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<.<<......
..>>.>>>>>.....>>>>>>>>...<<<.....>>>......>>>>>>.
......>>>..<<<<......<<<<<....>>>>>.<.<<<<<<...<<<
<<.<.<<....<......<<.<<<<...<<..<.........>...>>..
.>>>>.>>......>.....>>.>>>.>>>...>>>>>>..>...<<<<<
..<<<......>>>..>>>>>....<<<......>>>...<<<<.<<<..
.<<<((......<<.<<<...........<<..<<<<<...<........
.<.....<.....................>....................
......>.....>...>>>>>.>>............)).....>>>.>>.
>>>...>>>>>>><<<.<<<<......>>>>.>>>......>>>>..<<<
<<...<<<<.....<<<<<<<<....>>>>>>>>..>>>>..>>>>>...
.....>>>>>><......<<.....<<<<<<.......>>>>>><<<<..
..<<<<..<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<
.<..<<<...<<<....>>>...>>>...>>>...<<<<........>>>
>.))<<<<<<<<<<.<<...<<<<....<<<<..<<<..<<<<<<<<<<<
....(((...>>>>>><<..<<<..<.<<<<<<<<<<<<..........>
>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>
>...>>>...>>>.>........>>>>...>>.....>>>>>>>>>>.>>
>..>>.....<<......>>.>>>>.<<<<.....>>>>..>>>>..<<<
<....<<<<<<<...<...............<<<<<....<<..>>....
.>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
...<<......>>.......>>>>>>>..<<<<..<<..<<<<<<<..<<
<........<...<<.<<....>>..>>...>........>>>>>>>>..
>>>>.<<<<<<.......>>>>>>....................<<<<<.
......>>>>>..........>>>>...>>.>>>>>>>.....>...>>>
>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<
.(((.[[......<<<<.[.<<<<..<<<<..<<<.<<<<<.<<<<<<.<
<<<..<<............<<<<...<<.......<<.<<<<......>>
>>.>>....>>.............>>>.>..>.>.>>>>.>>>>>>...<
<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>...>>>>..<<<<.
....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<
<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<
..<<<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<<
<.((..>>>>..))>>>>>>>.............>>>>...]>>>>....
...<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>..
.....<<<<<.<<<<<<..<<<<<.<<<......>>>.>>>..>>.<<<<
<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>
>.>>>>....]]..)))>>>>>>>>....<<.<<<<...<<<<..<<<<<
<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<.<
.)))..>.>>>..>>>>>...>>>>.>>>>>...<<<.<..<<<<<....
.......>>>>>...>>>>.>>>>.......>>>>..>>.<<<<<.....
>>>>>.....<<..<<<<.........>>>>....<<.<<..<..<<...
.<<<<<....>>>>>...>>....>.>>..>>.....>>.....>>>>>>
>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6q97 How a circularized tmRNA moves through the ribosome.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		K6 H7 R8 H9 R11 S13 K16 R18 R25 K41 E52 S53 N57 N61 D77 E78 P80 R84 M86 P87 R88 A89 K90 G91 R92 D94 I96 L97 K98 R99
Binding residue
(residue number reindexed from 1)		K4 H5 R6 H7 R9 S11 K14 R16 R23 K39 E50 S51 N55 N59 D75 E76 P78 R82 M84 P85 R86 A87 K88 G89 R90 D92 I94 L95 K96 R97
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 11:48:29 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 = '6q97', asym_id = 'S', bs = 'BS01', title = 'How a circularized tmRNA moves through the ribosome.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6q97', asym_id='S', bs='BS01', title='How a circularized tmRNA moves through the 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 = '0003735,0005840,0006412,0015934', uniprot = '', pdbid = '6q97', asym_id = 'S'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0015934', uniprot='', pdbid='6q97', asym_id='S')
    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>