Structure of PDB 4v4n Chain AN Binding Site BS01

Receptor Information
>4v4n Chain AN (length=168) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRPAKIDRYVDKPAYTRREYIRGAPGPKITIFDMGNPAGDFEFEVSLHTA
EPVQIRQNALEAARQQVNRYLQKNVGRSNYHFKIRVYPFQVLRENPMATG
RKADRYGNGMRRPFGKPIGLAARLKKDQKILSIRVNRQHLKFAIEGARRA
AMKFPCKCYYRIYDKEGN
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)
R4 A6 K7 R10 K14 P15 A16 Y17 R19 E21 Y22 R24 F34 D35 R58 N60 A64 Q68 R71 K75 R87 Y89 F91 R95 N97 M99 R103 K104 R107 Y108 G109 G111 M112 R113 R114 P115 F116 G117 R150 R151 M154 K155 P157 Y161 R163
Binding residue
(residue number reindexed from 1)
R2 A4 K5 R8 K12 P13 A14 Y15 R17 E19 Y20 R22 F32 D33 R56 N58 A62 Q66 R69 K73 R85 Y87 F89 R93 N95 M97 R101 K102 R105 Y106 G107 G109 M110 R111 R112 P113 F114 G115 R148 R149 M152 K153 P155 Y159 R161
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Mar 7 09:04:17 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 = 'AN', 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='AN', 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 = 'AN'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v4n', asym_id='AN')
    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>