Structure of PDB 4v4n Chain Aj Binding Site BS01

Receptor Information
>4v4n Chain Aj (length=94) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYPKQIRTYCPFCKKHTIHKVERVKKRPRSELSAGQRRFRRILKGYGGF
PRPKPEGREKPVKKLDLRFRCTECGKAHTRGRGFRVKKFELVEG
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 K2 Y3 R8 T9 Y10 K15 K16 H17 K26 K27 R28 R30 E32 S34 A35 G36 R38 R39 R41 R42 L44 K45 Y47 G48 G49 F50 R52 P55 E56 G57 R58 E59 K60 P61 V62 K63 K64 D66 R68 K76 A77 T79 R80 G81 F84 R85 K88
Binding residue
(residue number reindexed from 1)
M1 K2 Y3 R8 T9 Y10 K15 K16 H17 K26 K27 R28 R30 E32 S34 A35 G36 R38 R39 R41 R42 L44 K45 Y47 G48 G49 F50 R52 P55 E56 G57 R58 E59 K60 P61 V62 K63 K64 D66 R68 K76 A77 T79 R80 G81 F84 R85 K88
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Mar 7 09:01:48 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 = 'Aj', 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='Aj', 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 = '0003735,0005840,0006412', uniprot = '', pdbid = '4v4n', asym_id = 'Aj'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v4n', asym_id='Aj')
    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>