Structure of PDB 4v95 Chain CH Binding Site BS01

Receptor Information
>4v95 Chain CH (length=138) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYER
VDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEI
PRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW
Ligand information
>4v95 Chain CA (length=1461) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcguggucagcggcggacgggugaguaacgc
gugggugaccuacccggaagagggggacaacccggggaaacucgggcuaa
ucccccauguggacccgccccuugggguguguccaaagggcuuugcccgc
uuccggaugggcccgcgucccaucagcuaguuggugggguaauggcccac
caaggcgacgacggguagccggucugagaggauggccggccacaggggca
cugagacacgggccccacuccuacgggaggcagcaguuaggaaucuuccg
caaugggcgcaagccugacggagcgacgccgcuuggaggaagaagcccuu
cgggguguaaacuccugaacccgggacgaaacccccgacgaggggacuga
cgguaccgggguaauagcgccggccaacuccgugccagcagccgcgguaa
uacggagggcgcgagcguuacccggauucacugggcguaaagggcgugua
ggcggccuggggcgucccaugugaaagaccacggcucaaccgugggggag
cgugggauacgcucaggcuagacggugggagagggugguggaauucccgg
aguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaaggca
gccaccugguccacccgugacgcugaggcgcgaaagcguggggagcaaac
cggauuagauacccggguaguccacgcccuaaacgaugcgcgcuaggucu
cugggucuccugggggccgaagcuaacgcguuaagcgcgccgccugggga
guacggccgcaaggcugaaacucaaaggaauugacgggggcccgcacaag
cgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuaccaggc
cuugacaugcccgggugaaagccugggcacaggugcugcauggccgucgu
cagcucgugccgugagguguuggguuaagucccgcaacgagcgcaacccc
cgccguuaguugccagcgguucggccgggcacucuaacgggacugcccgc
gaaagcgggaggaaggaggggacgacgucuggucagcauggcccuuacgg
ccugggcgacacacgugcuacaaugcccacuacaaagcgaugccacccgg
caacggggagcuaaucgcaaaaaggugggcccaguucggauuggggucug
caacccgaccccaugaagccggaaucgcuaguaaucgcggaucagccaug
ccgcggugaauacguucccgggccuuguacacaccgcccgucacgccaug
ggagcgggcucuacccgaagucgccgggagccuacgggcaggcgccgagg
guagggcccgugacuggggcgaagucguaacaagguagcuguaccggaag
gugcggcugga
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<
<.<<<..<<<..<<.<<<<<..>>>>>.>>>>>......<<.......<<
<<<<<<..<<...<<<<<<<.<<<<<....<<<<<......>>>>>....
.>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<<...>>>>.>
>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<.......>>>>>
>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<<<<<.
<.........>>>>>>.<<<<....>>>>...>>>>>>>........<<<
....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<<<..
..>>>>.....>>>>....<<<<<......<.<<<<.....>>>>..>..
.....>>>>>......<<<<<(((...<<<<<.....<<.)))>>.....
..>>>>>>>>>>..>>>>>>>>>..........<<<((.....<<<<...
<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>>....>
>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<<<<<<<
.<..<<<......>>>.....>.>>>>>>>...........<<....>>.
>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<...<<...<
<<<.<.....>.>>>>...>>>>>>>>..........<<<<<<..<<<<<
<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<..
....<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<.<<.<<
<<<<..<<<<<<<<<<......<<........>>..........<<<<<<
<......<<<<<<<<<....>>>>>>>>>.<<<.<<<..<<<<<<.....
..<<<<<<<<<....>>>..<<<<......>>>>..>>>>>>.....<<<
<.<<<<<<<...<...<<<.....>>>>.....>>>>>>>.....<<<<<
....>>>>>........>>>>.........>>>...>>>>>>>>>...>>
>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<..<<..<<<<.
...>>>>..>>....>>>.....>>>>>>>......<....<<<<<<<..
......>>>>>>>....>.....>>>>>>....<<<<<<<..........
>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<
<..<<<<<<<<<<<<<...<.<<<<....<<<....>>>.>>>>.>..>>
>>>>>>>>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>
>>>>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		M1 T3 P5 A7 T11 R12 R14 N15 V19 K21 A28 S29 R30 F31 R75 K88 P89 G90 R91 R92 Y94 R105 S113 T114 S115 G130 E132
Binding residue
(residue number reindexed from 1)		M1 T3 P5 A7 T11 R12 R14 N15 V19 K21 A28 S29 R30 F31 R75 K88 P89 G90 R91 R92 Y94 R105 S113 T114 S115 G130 E132
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Tue Mar 11 00:45:01 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 = 'CH', 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='CH', 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 = 'CH'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v95', asym_id='CH')
    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>