Structure of PDB 4v4n Chain AQ Binding Site BS01

Receptor Information
>4v4n Chain AQ (length=150) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNTLKMQRRIAAEILKCGENRIWIDPERIDDVASAITREDIKRLIKEGVI
KKKPIKGQSRYRAKIRHEQKKKGRHRGPGSRKGKKTARMGKKELWIKTIR
ALRKELRKLKAQKKIDRKTYRMLYIRAKGGQFKNKHQLYLFLEEHGLLKK
Ligand information
>4v4n Chain A1 (length=2969) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggacgcuaagccgcccgguggauggcucggcucggggcgccgacgaaggg
cguggcaagcugcgauaagccccggcgaggcgcaggcagccgucgaaccg
gggauucccgaaugggaccucccgcggcuuaugccgcacuccgaggggga
acgcggggaauugaaacaucuuaguacccgcaggaaaagaaagcaaaagc
gaugccgugaguaggggcgaccgaaaacggcagagggcaaacugaacccc
gggccgacgagguucgggggaugugggguuguagggcccccguaugagac
ccucgcgggugaagccgaaguccgcuggaacgcggcgccggagaggguga
uagccccguaggcguaagcccgcagggucucgggggacccugaguaccgu
cgguuggauauccggcgggaagcugggaggcaucggcucccaacccuaaa
uacgucccgagaccgauagcgaacuaguaccgugagggaaagcugaaaag
caccccgggaggggggugaaaagagccugaaaccgggcggcgauaggagg
gugcggcccgaaaggaaugagccuccccgaaggaaaccgcggcgacgcgg
gaguacgaggggaggggaccgggguugcaccguccgucuugaaacacggg
gcagggaguucgcggccguggcgagguuaaggggguuaagccccguagcc
gcagggaaaccgacaugcccgcagccgggccggugaggggcggggugcga
aagcgcccggagucacggccgcgagacccgaaaccggucgaucuagcccg
gggcagggugaagucccucaaccgagggauggaggcccgcuaggggugcu
gaugugcaguucgcucccgugaccccgggcuaggggugaaaggccaaucg
aggccggagauagcugguucccgccgaaucaucccgcaggauggccuccc
cggagguaggcggugggguagagcacugauuggaggugcagggggcgaaa
gcccccggccuccugucaaacuccgaacccaccgccgccguagauggggg
gaguaggguggcgguguaagccguccaccgagaggggaacaacccagacc
gggguuaaggccccaaagugccggcuaaguguuacuccaaaggguguccc
gggccuuagacagcggggagguaggcuuagaagcagccauccuuuaaaga
gugcguaacagcucacccgucgagguccggggccccgaaaauggacgggg
cucaagccggccgccgagaccccggcgcacggagugaucggguaggcggg
cgugccgguggcguagaagccgggccguaagguccgguggagccgccggu
aucgcggauccugccgggaguagcagcguagucgggugagaaucccgacc
gccggaggggccaggguuccacggcaauggucgucagccguggguuaguc
gguccuaaccccgcccguaacucggcgcgggggaaagggaaacggguuua
uauucccguaccgcggggguaggugcggcaacgcaagcccggagggugac
gccucgggguaggcggaccggccgaugaggccggcuaagcguauaagccc
ggggagugccguaauggcgagaaccgggugaaagcgcgaauggccccccc
guuagggggguuccgccgaucccuggggcccgugaaaagcccuccgggaa
uuccgaucccccgcgaccguaccgagaaccgacacaggugccccugggug
agaagccuaaggcgugucgggggaaacccggccgagggaacucggcaaac
uggccccguaacuucgggagaaggggugccugcgggugcguaacccgcag
gucgcagugacuaggggggcccgacuguuuaauaaaaacacaggucccag
cuagcccgaaaggguuuguacuggggccgacgccugcccagugccgguau
gugaagcccggguacaaccgggugaagcaccgguaaacggcggggguaac
uauaacccucuuaagguagcgaaauuccuugucgguuaaaugccgaccug
caugaauggcguaacgagguccccgcuguccccggccggggcccggcgaa
accucugccuggcgcgcaugccagggacccccggugggaagcgaagaccc
cauggagcuuuacugcagccugccguugccacacggcggggggugcgcag
cguaggcgggaggcgucgaagcccggccuccgggucggguggagccgucc
augagacaccgcccacuccccgcuguguggcuaacccccgaaagggggga
cagcgguaggugggcaguuuggcuggggcggcacgccuccgaaaagguau
cggaggcgcccuaaggucggcucaggcgggucaggaauccgccguagagu
gcaagggcaaaagccggccugacuggacccguaacagaggcggguccagc
cccgaaaggguggccuagcgaaccccugugccuccccggugggggccagg
gaugacagaaaagcuacccuggggauaacagagucgucucgggcgagagc
ccauaucgaccccgaggcuugcuaccucgcugucggcucuucccauccug
gcccugcagcaggggccaaggguggggguguucacccauuaaaggggaac
gugagcuggguuuagaccgucgugagacaggucggaugcuaucuaccggg
gguguuggccgccugaggggaaggugccccuaguacgagaggaacagggu
gccgcggccucuggucuaccgguuguccucccgggcaucgccgggcagcu
acgccgcagccgauaaggccugaaagcaucuaaggccgaagcggcccccg
aaaauaggcggccguggacgagggcucggguagaagacccgguugauagg
gcggggauguaagcgggaagggucaaccgacccgcuuaguccgccgcccc
uaaucgcccgagguccugc
<<.......<<<<<<<<<<.....<<..<<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<...<<<))..)).>>>......>>>
>>>...>>>....<<<...>>>.<<<<<....>>>>>.<<...>>.>>..
.<<<<<<.....<......>......>>>>>.>.........<<....>>
..<<<<<<.....<<.....>>....>>>>>>..<<<....<<...<<<<
<<<<<.....>>>>>>>>>.....>>..........<<<.<.......<<
<<<.<<<<<<...<<<.....<<<<......>>>>.((......<<<...
..))>>>...>>>....>>>>>>>>>>>...>>>>...........<<<<
<<<........>>>>>>>......<<<<<.((((((>>>>>..>>>....
..>>>>>>>>>.>>...............<<....>>....>>.......
..<<<<.....>>>>................>>>>>>>>>>........<
<<<<<<<<<....<<......<<<<<<<........<<<<<....>>>>>
........>>>>>>>...>>.>>>>>>>>>>..<<<<........>>>><
<<<<<....<<<<<<<<<<<<<..<<<....<<<<.....>>>>...>>>
...<<....>>....<<<<<...<<<<<.>>>>>...>>>>><<<<<<..
..>>>>>>...>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<
<<<..<<<....<<<<<<<....>>>>>>>.....>>>....<<<<.<<.
<<........>>>>>>>>....>>>>>>>>>...<<<.....>>>.....
.>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>><<<<<<<
<<..<<<.<<<<<<<<<...<<<....<<.....<..<<..<<<<.....
..>>>>.>>.>....>>...>>.>...>>>>>>>>>>>>.....>>>>>>
>.>>.<<..<<<<<<....>>>>>>..>>....<<<......>>>...<<
<<<<<...<<<(((.....<<<<<<.....<<.........<<<.<<<<<
<<<<........<<<<<.<<...<<<<.......>>>>...>>.......
..<<......>>...>>>>>....>>>>>>>>>>>>..........)))>
>....>>>>>>.>>>...>>>>>>><<<<<...>>>..>>....>>>>>>
<.<<<<<<<<<<......<<<<<<<<....>>>>>>>>...>>>>>>>>>
>..>.....>>>>>><<.....<<......<<<<<<.......>>>>>><
<<<....<<<<..<<...<<<<<<...<<.....>>.>>>>>>....((<
<<<<<...<<<<<<<<<.....>>>.>>>>>>....>>>..<<<<<....
....>>>>>))<<<<<<<<.....<<<....>>>......<<<<<<<...
<<<<<<<<<...<..<.<<<<<<.....>>>>>><...<<<<....<<<<
<<.....<<<<...>>>>.....>>>>>>....>>>>....><.<<<<<<
....>>>>>>.>.>..>...>>>>>>>>>.........>>>>>>>.....
.......>>>>>>>>.>>>..>>.....<<......>>.>>>>..<<<<.
....>>>>..>>>>...<<<<.....<<<<<<<<.<<.............
..<<<<<...............>>>>><<<<<<<<<<.....>>>>>>>>
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
...<<<<....>>>>......>>>>>>>.<<<<<.<<<..<<<<<<<..<
<<...<<<<<<......>>>>>>...>>>>>>>>..>>>>><<<<<<...
....>>>>>>........<...........<<<<<<.....>>>>>>...
..>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>...
.>>....<<<<<........>>>>>..<<<<<<<<.<<<.<<......<<
<<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<<<<<<......
....<<<<<...<.......<<<<<<<<....>>>>>>>>....>.....
........>>>>>.>>>>>>>>>>>>>>>>>...<<<<<....>>>>>..
..>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<..........
.>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<
...(((>>....>>>>>>>...<<<<<<<<<.........>>>>>>>>>.
<<<....>>>.>>))).......<<<<<.<<<<<.))))))>>>>>>>>>
>..........>>>>..>>>>>>.......<<<<.<.<<<<<<...<<..
.....>>...>>>>>>...>>>>.>.......<<<<<.<<<<<<..<<<<
<<<<<......>>>>>>>..>>..<<<.......>>>......>>>>>..
>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>>>>>>>
>>....<<<<<<<<..<<<<..<<<<<<<.................>>>>
>>><<<<<....<<<...<<<<<<<<<<....>>>>>..>>>>>...>>>
..>>>>>..<<<....<<<<<...........>>>>>....>>>.>>>>>
......>>>>>>>........<<<<<<<<<.......>>>>>....<<<<
<<<<<<<<....<<<<<..<<.....>>..>>>>>...>>>>.>>>>>.>
>>...>>>>.....>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v4n Structure of the SecY channel during initiation of protein translocation.
Resolution9.0 Å
Binding residue
(original residue number in PDB)
M1 K5 R8 W23 I24 I29 R38 E39 K42 R43 K46 E47 I55 K56 G57 Q58 S59 R60 Y61 R62 A63 K64 R66 H67 Q69 K70 K71 R74 H75 R76 P78 G79 S80 R81 K82 G83 K84 K85 T86 A87 R88 K91 K92 W95 R100 R103 R107 K110 R117 R121 Y124 I125 K128 G129 Q131 K135 H136
Binding residue
(residue number reindexed from 1)
M1 K5 R8 W23 I24 I29 R38 E39 K42 R43 K46 E47 I55 K56 G57 Q58 S59 R60 Y61 R62 A63 K64 R66 H67 Q69 K70 K71 R74 H75 R76 P78 G79 S80 R81 K82 G83 K84 K85 T86 A87 R88 K91 K92 W95 R100 R103 R107 K110 R117 R121 Y124 I125 K128 G129 Q131 K135 H136
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Mar 7 09:11:05 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 = '4v4n', asym_id = 'AQ', bs = 'BS01', title = 'Structure of the SecY channel during initiation of protein translocation.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4v4n', asym_id='AQ', bs='BS01', title='Structure of the SecY channel during initiation of protein translocation.')
   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 = '0003723,0003735,0005840,0006412,0022625', uniprot = '', pdbid = '4v4n', asym_id = 'AQ'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003723,0003735,0005840,0006412,0022625', uniprot='', pdbid='4v4n', asym_id='AQ')
    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>