Structure of PDB 4v4a Chain AL Binding Site BS01

Receptor Information
>4v4a Chain AL (length=124) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRK
VAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGV
YDAAGVKDRKKSRSKYGTKKPKEA
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)		P5 T6 N8 Q9 L10 R12 K13 R15 E16 K17 K21 K28 G29 P31 F32 R33 N49 S50 A51 L52 R53 K54 Y69 P71 G72 E73 R86 V90 K91 D92 R97 R113 K114 K115 R117 S118 K119 Y120 T122 K123 K124
Binding residue
(residue number reindexed from 1)		P1 T2 N4 Q5 L6 R8 K9 R11 E12 K13 K17 K24 G25 P27 F28 R29 N45 S46 A47 L48 R49 K50 Y65 P67 G68 E69 R82 V86 K87 D88 R93 R109 K110 K111 R113 S114 K115 Y116 T118 K119 K120
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 29 23:52:10 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 = 'AL', 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='AL', 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 = '0003735,0005840,0006412,0015935', uniprot = '', pdbid = '4v4a', asym_id = 'AL'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0015935', uniprot='', pdbid='4v4a', 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>