Structure of PDB 4v4a Chain AI Binding Site BS01

Receptor Information
>4v4a Chain AI (length=127) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLR
AVDALGRFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGF
LTRDARVVERKKYGKHKARRAPQYSKR
Ligand information
>4v4a Chain AA (length=1533) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uggagaguuugauccuggcucagggugaacgcuggcggcgugccuaagac
augcaagucgugcggauacgcgcggccccuuggggccgugcgucagcggc
ggacgggugaguaacgcgugggugaccuacccggaagagggggacaaccc
ggggaaacucgggcuaaucccccauguggacgcaaguccaaagggggaag
ccuucgggucccccgcuuccggaugggcccgcgucccaucagcuaguugg
ugggguaauggcccaccaaggcgacgacggguagccggucugagaggaug
gccggccacaggggcacugagacacgggccccacuccuacgggaggcagc
aguuaggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuu
ggaggaagaagcccuucgggguguaaacuccugaacccgggacgaaacca
gggccacucauacuggcucugacugacgguaccgggguaauagcgccggc
caacuccgugccagcagccgcgguaauacggagggcgcgagcguuacccg
gauucacugggcguaaagggcguguaggcggccuggggcgucccauguga
aagaccacggcucaaccgugggggagcgugggauacgcucaggcuagacg
gugggagagggugguggaauucccggaguagcggugaaaugcgcagauac
cgggaggaacgccgauggcgaaggcagccaccugguccacccgugacgcu
gaggcgcgaaagcguggggagcaaaccggauuagauacccggguagucca
cgcccuaaacgaugcgcgcuaggucucuggcggcucaaccgcugggggcc
gaagcuaacgcguuaagcgcgccgccuggggaguacggccgcaaggcuga
aacucaaaggaauugacgggggcccgcacaagcgguggagcaugugguuu
aauucgaagcaacgcgaagaaccuuaccaggccuugacaugcuagggaac
ccgggugaaagccuggggugccuucgggagcccuagcacaggugcugcau
ggccgucgucagcucgugccgugagguguuggguuaagucccgcaacgag
cgcaacccccgccguuaguugccagcgguucggccgggcacucuaacggg
acugcccgcgaaagcgggaggaaggaggggacgacgucuggucagcaugg
cccuuacggccugggcgacacacgugcuacaaugcccacuacaaagcgau
gccacccggcaacggggagcuaaucgcaaaaaggugggcccaguucggau
uggggucugcaacccgaccccaugaagccggaaucgcuaguaaucgcgga
ucagccaugccgcggugaauacguucccgggccuuguacacaccgcccgu
cacgccaugggagcgggcucuacccgaagucgccggguaaccuacgggaa
gcaggcgccgaggguagggcccgugacuggggcgaagucguaacaaggua
gcuguaccggaaggugcggcuggaucacuuucu
....<<<<....((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<<
.<<<..<<<..<<.<<..<<<<<<<<<<....>>>>>>>>>>>>.>>>>>
......<<.......<<<<<<<<..<<...<<<<<<<.<<<<<....<<<
<<<....>>>>>>.....>>>>>...<<<<<....>>>>>..<<<<<<..
<<....>>>>>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<
<<<<.......>>>>>>>>>>>......>>>..<<<<<<<<....>>>>.
..>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>...>>
>>>>>........<<<....<<<<....>>>>..>>>..>>.>>>>>>..
<<<<......<<<<....>>>>.....>>>>....<<<<<........<<
<<<<<<.......>>>>>>>>..........>>>>>......<<<<<(((
...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>>>>>>>.
.........<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<<..
....<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>>...<<<
<<<<<...<<<<<<<....<<<<<<<.<..<<<......>>>.....>.>
>>>>>>...........<<....>>.>>>>>>>..>>>>>.>>>...>>>
...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>...>>>>>
>>>..........<<<<<<..<<<<<<<<<<<<.....>>>>>>>>>>>>
...<<..))>>.....>>>>>>.>>>.<<<......<<<<....>>>>..
..>>>..))))..<<<<<.<<<<<<<.<<.<<<<<<..<<<<<<<<<<..
....<<........>>..........<<<<<<<......<<<<<<<<..<
<<<<<<....>>>>>>>...<<....>>..>>>>>>>>.<<<.<<<..<<
<<<<.......<<<<<<<<<....>>>..<<<<......>>>>..>>>>>
>.....<<<<.<<<<<<<...<...<<<.....>>>.>....>>>>>>>.
....<<<<<....>>>>>........>>>>.........>>>...>>>>>
>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<..
<<..<<<<....>>>>..>>....>>>.....>>>>>>>......<....
<<<<<<<........>>>>>>>....>.....>>>>>>....<<<<<<<.
.........>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.
<.<<<<.<<...<<<<<<<<<<<<<...<.<<<<......<<....>>..
...>>>>.>..>>>>>>>>>>>>>...>>.>>>>..>.>>...>.....<
<<<<<<<<....>>>>>>>>>............
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v4a X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli
Resolution9.5 Å
Binding residue
(original residue number in PDB)		Q3 Y5 T7 R9 R10 K11 E12 V14 R16 F18 R20 Y36 G39 Y62 R66 G67 G68 G69 K70 S71 G72 Q73 R83 R93 K97 T103 R104 A106 R107 V108 V109 E110 R111 K112 K113 Y114 G115 H117 K118 R120 R121 P123 Q124 Y125 S126 K127 R128
Binding residue
(residue number reindexed from 1)		Q2 Y4 T6 R8 R9 K10 E11 V13 R15 F17 R19 Y35 G38 Y61 R65 G66 G67 G68 K69 S70 G71 Q72 R82 R92 K96 T102 R103 A105 R106 V107 V108 E109 R110 K111 K112 Y113 G114 H116 K117 R119 R120 P122 Q123 Y124 S125 K126 R127
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon Dec 2 03:33:21 2024

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 = '4v4a', asym_id = 'AI', bs = 'BS01', title = 'X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4v4a', asym_id='AI', bs='BS01', title='X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli')
   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 = '4v4a', asym_id = 'AI'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v4a', asym_id='AI')
    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>