Structure of PDB 5fdu Chain 1n Binding Site BS01

Receptor Information
>5fdu Chain 1n (length=60) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKG
QLPGVRKASW
Ligand information
>5fdu Chain 1a (length=1500) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag
uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg
ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu
gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug
gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca
ggggcacugagacacgggccccacuccuacgggaggcagcaguuaggaau
cuuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaa
gcccuucgggguguaaacuccugaacccgggacgaaacccccgacgaggg
gacugacgguaccgggguaauagcgccggccaacuccgugccagcagccg
cgguaauacggagggcgcgagcguuacccggauucacugggcguaaaggg
cguguaggcggccuggggcgucccaugugaaagaccacggcucaaccgug
ggggagcgugggauacgcucaggcuagacggugggagagggugguggaau
ucccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcg
aaggcagccaccugguccacccgugacgcugaggcgcgaaagcgugggga
gcaaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcu
aggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgcc
uggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccg
cacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuua
ccaggccuugacaugcuagggaacccgggugaaagccuggggugccccgc
gaggggagcccuagcacaggugcugcauggccgucgucagcucgugccgu
gagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugc
cagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggagga
aggaggggacgacgucuggucagcauggcccuuacggccugggcgacaca
cgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcua
aucgcaaaaaggugggcccaguucggauuggggucugcaacccgacccca
ugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauac
guucccgggccuuguacacaccgcccgucacgccaugggagcgggcucua
cccgaagucgccgggagccuacgggcaggcgccgaggguagggcccguga
cuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggauc
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<
<.<<<..<<<..<<.<<<<<<<<..>>>>>>>>.>>>>>......<<...
....<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<......>>>
>>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<<...
>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<......
.>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.
<<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>>.....
...<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......
<<<<....>>>>.....>>>>....<<<<<........<<<<.....>>>
>..........>>>>>......<<<<<(((...<<<<<.....<<.)))>
>.......>>>>>>>>>>..>>>>>>>>>..........<<<((.....<
<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>
>....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<
<<<<<<.<..<<<......>>>.....>.>>>>>>>...........<<.
...>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<...
<<...<<<<.........>>>>...>>>>>>>>..........<<<<<<.
.<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>>
.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<
.<<.<<<<<<..<<<<<<<<<<......<<........>>..........
<<<<<<<......<<<<<<<<..<<<<<<<....>>>>>>>.<.<<<...
...>>>>.>>>>>>>>.<<<.<<<..<<<<<<.......<<<<<<<<<..
..>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<<<..<<
<..<<<.....>>>>>>...>>>>>>>.....<<<<<....>>>>>....
....>>>>.........>>>...>>>>>>>>>...>>>>>>>...>>.>>
>>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>..>>..
..>>>.....>>>>>>>...........<<<<<<<........>>>>>>>
..........>>>>>>....<<<<<<<..........>>>>>>>......
>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<<
<<<...<.<<<<....<<<....>>>.>>>>.>..>>>>>>>>>>>>>..
>>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>>.....
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5fdu Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		A2 R3 K4 A5 L6 E8 K9 F16 K17 V18 R19 Y21 C27 R29 R31 S32 Y34 R35 R41 I42 R45 E46 K58 S60 W61
Binding residue
(residue number reindexed from 1)		A1 R2 K3 A4 L5 E7 K8 F15 K16 V17 R18 Y20 C26 R28 R30 S31 Y33 R34 R40 I41 R44 E45 K57 S59 W60
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 16 00:52:19 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 = '5fdu', asym_id = '1n', bs = 'BS01', title = 'Structure of the mammalian antimicrobial peptide...d within the exit tunnel of a bacterial ribosome.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5fdu', asym_id='1n', bs='BS01', title='Structure of the mammalian antimicrobial peptide...d within the exit tunnel of a bacterial 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 = '5fdu', asym_id = '1n'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='5fdu', asym_id='1n')
    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>