Structure of PDB 6p5n Chain Aq Binding Site BS01

Receptor Information
>6p5n Chain Aq (length=416) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADE
FGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEG
KEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSG
ALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKV
AETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVD
ISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGV
EDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKS
HFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKG
FGGIGGILRYRVDFQG
Ligand information
>6p5n Chain 5 (length=3594) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugccggcggggcgga
ucucccgcucccgucggcgggggaccgccccccggccggcgaccggccgc
cgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacg
gcugggaaggcccggcggggaagguggcccgggggccccggguguuacag
cccacccggcagcagcagcucgccgaaucccggggccgagggagcgagac
cugugucgccgcgcucuccccccugggggggccgggccaccccucccacg
gcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgucccccgcgagcgcacggggucggcggcg
augucggcuacccacccgacccgucuugaaacacggaccaaggagucuaa
cacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaaggug
aaggccggcgccgccggccgaggugggaucccgaggccuuccaguccgcc
gagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagca
cgagcgcacguguuaggacccgaaagauggugaacuaugccugggcaggg
cgaagccagaggaaacucugguggagguccguagcgguccugacgugcga
aucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucua
guagcugguucccuccaaaguuucccucaggauagcuggcgcucuccgca
guuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucu
caaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggugug
gagccgggcguggaaugcgagugccuagugggccacuuuugguaagcaga
acuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccga
cgcucaucagaccccagaaaagguguugguugauauagacagcaggaugg
uggccauggaagucggaauccgcuaaggaguguguaacaacucaccugcc
gaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacc
cggccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgcu
acgccgcgacgaguaggagggccgcugcggugagccuugaagccuagggc
gcgggcccggguggagccgccgcaggugcagaucuuggugguaguagcaa
auauucaaacgagaacuuugaaggccgaaguggagaaggguuccauguga
acagcaguugaacaugggucagucgguccugagagaugggcgagcgccgu
uccgaagggacgggcgauggccuccguugcccucagccgaucgaaaggga
gucggguucagauccccgaauccggaguggcggagaugggcgccgcgagg
cguccagugcgguaacgcgaccgaucccggagaagccggcgggagccccg
gggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguuc
gccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcg
uccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaau
cucgcgccgggccguacccauauccgcagcaggucuccaaggugaacagc
cucuggcauguuggaacaauguagguaagggaagucggcaagccggaucc
guaacuucgggauaaggauuggcucuaagggcuggcagccgacuuagaac
uggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcga
aggcccgcggcggguguugacgcgaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacu
augacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgc
augaauggaugaacgagauucccacugucccuaccuacuauccagcgaaa
ccacagccaagggaacgggcuuggcggaaucagcggggaaagaagacccu
guugagcuugacucuagucuggcacggugaagagacaugagagguguaga
auaagugggaggcccgggccgccggugaaauaccacuacucugaucguuu
uuucacugacccggugaggcgggggggcgagccgggcucucgcuucuggc
gccaagcgcccggccggccgggcgcgacccgcuccggggacagugccagg
uggggaguuugacuggggcgguacaccugucaaacgguaacgcagguguc
cuaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaa
aagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggg
gccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaa
aguuaccacagggauaacuggcuuguggcggccaagcguucauagcgacg
ucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaa
uucaccaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugauguguuguu
gccaugguaauccugcucaguacgagaggaaccgcagguucagacauuug
guguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauag
cgccggagccucgguuggccucggauagccggucccccgccgggguccgg
ugcggagagcccuucgucccgggaaacggggcggccggaaagggggccgc
ccucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacc
auucguagacgaccugcuucugggucgggguuucguacguagcagagcag
cugcugcgaucuauugaaagucagcccucgacacaaggguuugu
.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<....<<<<<<<<..<<<<<<<<....<<<<..
....>>>>.....((......<<<.....))>>>...>.>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...<<<<<..((((((>>>>>..>>>........................
..........<<....>>...............<<<<....>>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<....<<<<<<<.<<<<<.<<<<<<<.
<<<<<<<.<<.....>>>>>>>>>>>>>>>>>>>>>>>>>...>>>..>>
>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<<<<
<<...<<..<<..<<..<<<......<<<<<<<..>.>>>>>>.......
>>>..>>.>>.........>>>>>>..>>>>>>>>>>>.....<<.....
<.>>......<<<<<<.<<<<<<..>>>>>>...<.<<..<<<.<<<<<<
<<<<<<<<<<<<<<<<<.<<<<..>>>>.>>>>>>.>>>.>>>>>>>>>>
>.>>>...>>>.>>>..............>>>>>>......>>.>>>>>.
...>>>>...>>>>>>>>..<<<<........>>>><<<<<<....<<<<
<<<<<<<<<..<<<...<<<.......>>>.....>>>...<<....>>.
..<<<<<<<...>>>>>>>..<<<<<...<<<..<<<....[[.[..>>>
..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>.
...>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<
....<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<.......
.>>>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>..
.>..>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<...<<<
.<<<<<<<<<...<<<....<<<..<.<<<<..<<<.<.........>.>
>>>>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<<<.<......>
>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>
>.>>>>....<<<......>>>...<<<<<<<...<<<(((.......<<
<<<.....<<..........<<<.<<<<<<<<<<..........<<.<<.
...<<.........>>....>>.........<<......>>...>>....
..>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>>
>>>><<<<<<.<<<........>............].]]...........
..>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<
....>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<<....<<..
...<<<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<<<<..
.<<.....>>.>>>>>>....(.<<<<<<...<<....<<<....>>>..
........<<.<<<<<.<<<...>>>.>>>>>>>......>>....>>>.
.<<<<<........>>>>>.)<<<<....<<<<<..<<<<<<<<....>>
>>>>>>..<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<
<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<<<<.....<<<...
..>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>
>>>>>...>>>>>>>>>>>>.........>>>>>>>..>..........>
>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<.....>>
>>..>>>....<<<<.....<<<<<<<.<<.........<.....<<<<<
....<<..>>.....>>>>><<.<<<<<<<<<<<.>>>>>..>>>>>>.>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
..<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....
<<<.....<<<<....>>>>.....>>>.>>>>..>>>>>.<<<<<....
...>>>>>.........<...........<<<<<.......>>>>>....
.>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>
>>....<<<<<........>>>>>....<<<<<..<<<.<<......<<<
<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<.<<<<.......
...<<<.....<<<..>>>...............>>>.>>>>.>>.>>>>
>>>>>>...<<<<<.....<<<<...<....<<>>....>..........
.....<<<<<<<<<..>>>>>>>>>..>>>>..>>>>>....>>>>>>>>
>..>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>..
..>>>>>>>...<<<..<<<<.......>>>>..>>>.<<<....>>>.>
>)))].....<<<<<<<..<<<..)))))).>>>>>>>>>>.........
>>>>..>>>>>>.......<<.<.<.<<<<<<...<<.......>>...>
>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<<<<......
>>>>>...>.>.<<<.........>>>.....>>>>>..>...>>>.>>.
...<<<<<<<....>>>.>>>>....>>..>>>.>>>>>.....<<<<<<
.<..<<<..<.<<<<<.................>>>>>.><<<<....<<
<<....<<.<<<<<<<]]].>>>>>..>>.>>...>>>>...>>>><<<<
....<<<<<...........>>>>>....>>>>.>>>...>.>>>>>>.<
<<<<<<..<<<<....<<<........<<<<<.<.<<<<.>>>>>.>>>>
>.......>>>...<<<..<<<<....<<....<.............>..
..>>...>>>>..>>>..............>>>>..>.>>>>>>.<<<<<
.<.............>....<<.<<<<<<<.<<.....<<<<.<..<<<<
<.>>>>>..>>>>>....>>....>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6p5n The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
K42 R47 N121 S123 Y125 G153 K178 K179 H180 R182 G183 Q185 L188 R189 R192 A230 D255 I256 S257 S295 K384 Y415
Binding residue
(residue number reindexed from 1)
K37 R42 N116 S118 Y120 G148 K173 K174 H175 R177 G178 Q180 L183 R184 R187 A225 D250 I251 S252 S290 K379 Y410
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Thu Apr 10 19:00:11 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 = '6p5n', asym_id = 'Aq', bs = 'BS01', title = 'The Israeli acute paralysis virus IRES captures ...by mimicking a ribosomal state with hybrid tRNAs.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6p5n', asym_id='Aq', bs='BS01', title='The Israeli acute paralysis virus IRES captures ...by mimicking a ribosomal state with hybrid tRNAs.')
   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 = '0003747,0006415', uniprot = '', pdbid = '6p5n', asym_id = 'Aq'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003747,0006415', uniprot='', pdbid='6p5n', asym_id='Aq')
    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>