Structure of PDB 4v4p Chain AL Binding Site BS01

Receptor Information
>4v4p Chain AL (length=133) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVV
ITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEE
IAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV
Ligand information
>4v4p Chain AA (length=2872) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuugcgcggggggaaccuggggaacugaaacaucucaguaccca
gaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaagggg
accagccuaaaccguccggcuuguccgggcggggucguggggcccucgga
caccgaauccccagccuagccgaagcuguugggaagcagcgccagagagg
gugaaagccccguaggcgaaagguggggggauaggugaggguacccgagu
accccgugguucguggagccaugggggaaucugggcggaccaccgccuaa
ggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagg
ugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuu
acaagcagucacggccccgcaagggguuguggcgugccuauugaagcaug
agccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcg
uagggaaaccgaguccgaacagggcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcc
auccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaugcggggcuuaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
aggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
ggggggccacccuggcgcggcugggggccuaacccucggauggggggaca
gcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacgg
aggcgcccaaagguccccucaggcgggacggaaauccgccggagagcgca
aggguagaagggggccugacugcgaggccugcaagccgagcaggggcgaa
agccgggccuagugaaccgguggucccguguggaagggccaucgaucaac
ggauaaaaguuaccccggggauaacaggcugaucucccccgagcguccac
agcggcggggagguuuggcaccucgaugucggcucgucgcauccuggggc
ugaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcga
gcuggguucagaacgucgugagacaguucggucucuauccgccacgggcg
caggaggcuugaggggggcucuuccuaguacgagaggaccggaagggacg
caccucugguuucccagcugucccuccaggggcauaagcuggguagccau
gugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaa
gaugaggccucccacggcgucaagccgguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccgaggucuugacc
<<<<<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<....
..<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>....
.>>>>>>>...>>>....<<<....>>><<<<<..........>>>>>..
<.<........>..>.>>...<<<<<<.....<......>......>>>>
>.>.........<<....>>...<<<<<.....<<.....>>....>>>>
>...<<<.....<<<<<<<.....>>>>>>>.......<<<<<<<.....
.......<<.<.......<<<...<<<<<......>>>>>((......<<
<.....))>>>...>>>.........>>>.........>>>>.>>>....
.<<<<<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..
>>>......>>.>>>>>>.>>...............<<....>>....>>
.........<<<<....>>>>..................>>>>>>>>>>>
.......<<<<<<<<<<<....>>>>>>>>>>>...<............>
.<<<<<<....<<<<<<<<<<<<<...<.....<......>.....>...
..<<....>>...<<......>>.......>>>>>>>>>>>>>..<<.<.
..<<<<<<....<<<<<<<<<<..<<<....<<<<<<......>>>>>>.
....>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>>.
.<<<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<
<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<
...<<<<<<......>>>>.>>...>>>>>>>>..>>.>...>>>>>>>>
>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<
<<......>>>...<<<..<<<...<<<((......<<<<<<<.......
...<<..<<<<<<..<........<<<<..<<...<<<.........>>>
...>>.........<........>....>>>>....>..>>>>>>.>>..
.........))......>>>>>>>.>>>...>>>.>>><<<<<<<.....
..>>>>>>>....>>>>>><<<<<<.....<.......<<<<<.<.....
.>.>>>>>....>....>>>>.>>.....>>>>>>.......<......<
<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<..
...>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>
...>>...<<<<<........>>>>>))<<<<<<<<<<<.<...<<<...
..<<<<<.<<...<<<<<.<<<<.<<...[[[...>>>>>><.....<<.
..<<.<<<<<<<...<......>.>>>>>>....>.>>..>>.....>..
.....................>>>>>....>>..>>>>>.........>>
>....>....>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.
<<<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<.........
<.....<<<<<...............>>>>><<<<<<<<<<........>
>>.>>>>>>>............<<<<<<<<<..<<<.........>>>..
<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<
<<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>>>>>>..
>>>>><<<<<<.......>>>>>>........<...........<<<<<<
.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>
>>>>.>>>>.>...........<<<<<........>>>>>..<<<<<<<<
.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<..<<<<<<<<
<<<<<<<<...........<<<...............<<..<<...>>..
.>>.....>>>..>>>>>>>>>>>>>>>>...<<<<......>>>>....
.>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<...........>>
>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<....
(((.>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<...
.>>>.>>))).......<<<<<<<.<<..))))..>>>>>>>>>......
.......>>>>..>>>>>>.......<<<<..<<<<<<<...<<......
.>>...>>>>>>>...>>>.>.......<.<<<.<<<<<<..<<<<<<<<
<......>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>..>...
>>>..>....<<<<<<<....>>>.>>>>........>>>>>>>>>>>..
..<<<<<<<...<<<<..<<<<<<<...............>>>>>>>.<<
<<<...<<<<...<<<<<<<<<<<]]].>>>>>>...>>>>>...>>>>.
>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>>..
.....>>>>>>>...<.<.....>>......<<<<<<<<<.......>>>
>>....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.
>>>...>>>>....>>>>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v4p Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding.
Resolution5.5 Å
Binding residue
(original residue number in PDB)
Q12 H31 P74 A75 S76 F77 K87 G88 S90 E91 P92 K93 R94 K112 D115 N117 A118 A123 K126 I127 E129 G130 T131 S134 M135
Binding residue
(residue number reindexed from 1)
Q5 H24 P67 A68 S69 F70 K80 G81 S83 E84 P85 K86 R87 K105 D108 N110 A111 A116 K119 I120 E122 G123 T124 S127 M128
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Mar 7 08:53:42 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 = '4v4p', asym_id = 'AL', bs = 'BS01', title = 'Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4v4p', asym_id='AL', bs='BS01', title='Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding.')
   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 = '4v4p', asym_id = 'AL'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v4p', asym_id='AL')
    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>