Structure of PDB 4v95 Chain AN Binding Site BS01

Receptor Information
>4v95 Chain AN (length=59) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQ
LPGVRKASW
Ligand information
>4v95 Chain AA (length=1466) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggccguggucagcggcggacgggugagua
acgcgugggugaccuacccggaagagggggacaacccggggaaacucggg
cuaaucccccauguggacccgccccuugggguguguccaaagggcuuugc
ccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaauggc
ccaccaaggcgacgacggguagccggucugagaggauggccggccacagg
ggcacugagacacgggccccacuccuacgggaggcagcaguuaggaaucu
uccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagc
ccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggga
cugacgguaccgggguaauagcgccggccaacuccgugccagcagccgcg
guaauacggagggcgcgagcguuacccggauucacugggcguaaagggcg
uguaggcggccuggggcgucccaugugaaagaccacggcucaaccguggg
ggagcgugggauacgcucaggcuagacggugggagagggugguggaauuc
ccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaa
ggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggagc
aaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuag
gucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccug
gggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgca
caagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuacc
aggccuugacaugcccgggugaaagccugggcacaggugcugcauggccg
ucgucagcucgugccgugagguguuggguuaagucccgcaacgagcgcaa
cccccgccguuaguugccagcgguucggccgggcacucuaacgggacugc
ccgcgaaagcgggaggaaggaggggacgacgucuggucagcauggcccuu
acggccugggcgacacacgugcuacaaugcccacuacaaagcgaugccac
ccggcaacggggagcuaaucgcaaaaaggugggcccaguucggauugggg
ucugcaacccgaccccaugaagccggaaucgcuaguaaucgcggaucagc
caugccgcggugaauacguucccgggccuuguacacaccgcccgucacgc
caugggagcgggcucuacccgaagucgccgggagccuacgggcaggcgcc
gaggguagggcccgugacuggggcgaagucguaacaagguagcuguaccg
gaaggugcggcuggau
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<
<.<<<..<<<..<<.<<<<<<<..>>>>>>>.>>>>>......<<.....
..<<<<<<<<..<<...<<<<<<<.<<<<<...<<<<<<......>>>>>
.>...>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<<...>>
>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<.......>
>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<<
<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>>.......
.<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<
<<....>>>>.....>>>>....<<<<<........<<<<.....>>>>.
.........>>>>>......<<<<<(((...<<<<<.....<<.)))>>.
......>>>>>>>>>>..>>>>>>>>>..........<<<((.....<<<
<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>>.
...>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<<<
<<<<.<..<<<......>>>.....>.>>>>>>>...........<<...
.>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<...<<
...<<<<.<.....>.>>>>...>>>>>>>>..........<<<<<<..<
<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<
<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<.<
<.<<<<<<..<<<<<<<<<<......<<........>>..........<<
<<<<<......<<<<<<<<<....>>>>>>>>>.<<<.<<<..<<<<<<.
......<<<<<<<<<....>>>..<<<<......>>>>..>>>>>>....
.<<<<.<<<<<<<...<...<<<.....>>>>.....>>>>>>>.....<
<<<<....>>>>>........>>>>.........>>>...>>>>>>>>>.
..>>>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<..<<..<
<<<....>>>>..>>....>>>.....>>>>>>>......<....<<<<<
<<........>>>>>>>....>.....>>>>>>....<<<<<<<......
....>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<.<<<
<.<<<..<<<<<<<<<<<<<...<.<<<<....<<<....>>>.>>>>.>
..>>>>>>>>>>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<.
...>>>>>>>>>....
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v95 Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		R3 K4 A5 L6 E8 K9 F16 K17 V18 R19 Y21 T22 R29 A30 R31 S32 V33 R35 R41 I42 R45 E46 K58 S60 W61
Binding residue
(residue number reindexed from 1)		R1 K2 A3 L4 E6 K7 F14 K15 V16 R17 Y19 T20 R27 A28 R29 S30 V31 R33 R39 I40 R43 E44 K56 S58 W59
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Tue Mar 11 00:34:32 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 = '4v95', asym_id = 'AN', bs = 'BS01', title = 'Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4v95', asym_id='AN', bs='BS01', title='Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to 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', uniprot = '', pdbid = '4v95', asym_id = 'AN'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v95', asym_id='AN')
    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>