Structure of PDB 8g5y Chain Lm Binding Site BS01

Receptor Information
>8g5y Chain Lm (length=52) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKK
VK
Ligand information
>8g5y Chain L5 (length=3721) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggcgggggaccgucccccgaccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccugggggggccgggccaccccucccacggcg
cgaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgcgcgucccccgaagagggggacggcggag
cgagcgcacggggucggcggcgacgucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgag
gugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcagacccgacgccacgcaguuuua
uccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccu
auucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccg
ggcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggc
gcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcuca
ucagaccccagaaaagguguugguugauauagacagcaggacgguggcca
uggaagucggaauccgcuaaggaguguguaacaacucaccugccgaauca
acuagcccugaaaauggauggcgcuggagcgucgggcccauacccggccg
ucgccggcagucgagaguggacgggagcggcgggcccgcggacgcuacgc
cgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcgg
gcccggguggagccgccgcaggugcagaucuuggugguaguagcaaauau
ucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacag
caguugaacaugggucagucgguccugagagaugggcgagcgccguuccg
aagggacgggcgauggccuccguugcccucggccgaucgaaagggagucg
gguucagauccccgaauccggagcggagaugggcgccgcgaggcguccag
ugcgguaacgcgaccgaucccggagaagccggcgggagccccggggagag
uucucuuuucuuugugaagggcagggcgcccuggaauggguucgccccga
gagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccggug
agcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgc
cgggccguacccauauccgcagcaggucuccaaggugaacagccucuggc
auguuggaacaauguagguaagggaagucggcaagccggauccguaacuu
cgggauaaggauuggcucuaagggcugguagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagagguguagaauaa
gugggaggcccccggcgcccccccgguguccccgcgaggggcccggggcg
ggguccgccggcccugcgggccgccggugaaauaccacuacucugaucgu
uuuuucacugacccggugaggcgggggggcgagccccgaggggcucucgc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugacuggggcgguacaccugucaaacg
guaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgug
gagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacag
accgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagca
ggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaag
cguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauc
auugugaagcagaauucaccaagcguuggauuguucacccacuaauaggg
aacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacu
gaugauguguuguugccaugguaauccugcucaguacgagaggaaccgca
gguucagacauuugguguaugugcuuggcugaggagccaauggggcgaag
cuaccaucugugggauuaugacugaacgccucuaagucagaaucccgccc
aggcggaacgauacggcagcgccgcggagccucgguuggccucggauagc
cggucccccgcgggguccggugcggagugcccuucguccugggaaacggg
gcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguuc
guggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgg
gguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguca
gcccucgacacaaggguuugu
.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<...<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>...<<<<<<<<<<...<<<<<<<<.<<.....<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>.>>>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..((((((>>>>>..>>>..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<.<
<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<<<...
<<<<<.<<<..<<<...>>>>>>>>>>>..>>>..>>>>...>>>>>>>>
>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<<<<<
<...<<..<<<..<.<<<<......<<<<<<<<..>>>>>>>>.......
>>>>.>.>>>........>>>>>>..>>>>>>>>>>>.............
.......<<<<<<.<<<<<<..>>>>>>.<<<<<<.<<<<.<<<<<<<<<
<<<<<<<.<<<<<<<.<<<<....>>>>.>>>>>>>.>>>.>>>>>>>>>
>.>>>...>>>>>>>>.>>..<<<<<<<<<<.....>>>>>>>>.>>...
.>>>>>>......>>.>>>>>...>>>>>...>>>>>>>>..<<<<....
....>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<.......
.>>>>.....>>>...<<....>>...<<<<<<<<....>>>>>>>>..<
<<<<...<<<..<<<..((((.(((.>>>..>>>....>>>>>.<<<<<<
<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.
<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>
>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>
>...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<
.<<<....>>>.><<.<<<<<<<..................<<<.<<<<<
<<<<...<<<....<<<..<.<<<..<<<<<<.<<...>>.>>>>>>>>>
.>..>>>..>.>>...>>>>>>>...<<<<<<<<<.........>>>>>>
>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>
....<<<......>>>...<<<<<<<...<<<(((.......<<<<<...
..<<..........<<<.<<<<<<<<<<........<<<<.<<....<<.
........>>....>>.........<<......>>...>>>>....>>>>
>>>>>>>>>..........))).>>...>>>>>..>>>...>>>>>>><<
<<<<.<<<...........))).)))).....................>>
>>>>>>>....>>>>>>...<<<<<<<<.<<......<<<<.<<<<....
>>>>>>>>...>>>>>>>>>>........>>>>>><<.....<<.....<
<<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<.
....>>.>>>>>>....((<<<<<<...<<....<<<....>>>......
....<<.<<<<<<<<<...>>>>>>>>>>>......>>....>>>..<<<
<<........>>>>>))<<<<.<<<<<..<<<<<<<<....>>>>>>>>.
.<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<
..[[[..>>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>..
...>>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>..
.>>>>>>>>>>>>.........>>>>>>>..>..........>>.>>>.>
>>>.>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>
....<<<<.....<<<<<<<.<<...............<<<<<.......
........>>>>><<.<<<<<<<<<<<....>>>>>..>>>>>>.>>...
.........<<<<<<<<<..<<<.........>>>..<<<<<<<....<<
<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....<<<.
....<<<<....>>>>.....>>>.>>>>..>>>>><<<<<<.......>
>>>>>........<...........<<<<<.......>>>>>.....>..
...>>....>>.>>>>>>>.....>>.>>>>>>>..>>>>>>....>>..
..<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.<<
<<<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<.<<<<...........
<..<<.............................................
..................................>>..>.>>>>.>>.>>
>>>>>>>>...<<<<<.....<<<<..<<.<<............>>>>..
............<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>
>>....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<......
.....>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>...
..<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>
><<<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>
>>>>>.........>>>>..>>>>>>.......<<.<...<<<<<<...<
<.......>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<
.<.<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>
>..>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>
>>>.....<<<<<<.<..<<<....<<<<<.................>>>
>>..<<<<....<<<<....<<.<<<<<<<]]].>>>>>..>>.>>...>
>>>...>>>><<<<<...<<<<<...........>>>>>...>>>>>.>>
>...>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<
<<<.<<<<...>>>>.>>>>>.......>>>...<<<..<<<<....<<<
<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>............
..>>>>..>>>>>>>>><<<<<....................<<.<<<<<
<<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>...
.>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8g5y mRNA decoding in human is kinetically and structurally distinct from bacteria.
Resolution2.29 Å
Binding residue
(original residue number in PDB)
K93 R97 Y100 R102 H104 R106 V108 N109 R111 K112 K113 K114 G116 H117 N119 R122 K124 K125
Binding residue
(residue number reindexed from 1)
K17 R21 Y24 R26 H28 R30 V32 N33 R35 K36 K37 K38 G40 H41 N43 R46 K48 K49
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Feb 28 09:39:39 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>()
   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 = '8g5y', asym_id = 'Lm', bs = 'BS01', title = 'mRNA decoding in human is kinetically and structurally distinct from bacteria.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8g5y', asym_id='Lm', bs='BS01', title='mRNA decoding in human is kinetically and structurally distinct from bacteria.')
   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 = '8g5y', asym_id = 'Lm'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='8g5y', asym_id='Lm')
    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>