Structure of PDB 4v4n Chain BN Binding Site BS01

Receptor Information
>4v4n Chain BN (length=145) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKKAPNGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARG
IVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDE
VIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR
Ligand information
>4v4n Chain B2 (length=1495) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
auuccgguugauccugccggaggccacugcuauggggguccgacuaagcc
augcgagucaagggggcgucccuucugggacgccaccggcggacggcuca
guaacacgucgguaaccuacccucgggagggggauaaccccgggaaacug
gggcuaaucccccauaggccugggguacuggaagguccccaggccgaaag
ggagccguaaggcccgcccgaggaugcggcggcggccgauuagguaguug
gugggguaacggcccaccaagccgaagaucgguacgggccgugagagcgg
gagcccggagauggacacugagacacggguccaggcccuacggggcgcag
caggcgcgaaaccuccgcaaugcgggaaaccgcgacggggggacccccag
ugccgugccucuggcacggcuuuuccggaguguaaaaagcuccgggaaua
agggcugggcaaggccgguggcagccgccgcgguaauaccggcggcccga
gugguggccacuauuauugggccuaaagcggccguagccgggcccguaag
ucccuggcgaaaucccacggcucaaccguggggcucgcuggggauacugc
gggccuugggaccgggagaggccggggguacccccgggguaggggugaaa
uccuauaaucccggggggaccgccaguggcgaaggcgcccggcuggaacg
gguccgacggugagcgcggaaggccaggggagcgaaccggauuagauacc
cggguaguccuggcuguaaaggaugcgggcuaggugucgggcgagcuucg
agcucgcccggugccguagggaagccguuaagcccgccgccuggggagua
cggccgcaaggcugaaacuuaaaggaauuggcgggggagcacuacaaggg
guggagcgugcgguuuaauuggauucaacgccgggaaccucaccgggggc
gacggcaggaugaaggccaggcugaaggucuugccggacgcgccgagagg
aggugcauggccgccgucagcucguaccgugaggcguccacuuaagugug
guaacgagcgagacccgcgcccccaguugccagucccucccgcucgggag
gaggcacucuggggggacugccggcgauaagccggaggaaggggcgggcg
acgguaggucaguaugccccgaaacccccgggcuacacgcgcgcuacaau
gggcgggacaaugggacccgaccucgaaaggggaagggaauccccuaaac
ccgcccucaguucggaucgcgggcugcaacucgcccgcgugaagcuggaa
ucccuaguacccgcgugucaucaucgcgcggcgaauacgucccugcuccu
ugcacacaccgcccgucacuccacccgagcggaguccgggugaggccuga
ucuccuucgggaggucaggucgagcccgggcuccgugaggggggagaagu
cguaacaagguaaccguaggggaaccuacggcucgaucaccuccu
...<<<<<.[.((((>>>>>.<<<<<<<<<....<<<<.<<......<<<
.<<<..<<<..<<.<<<<<<<<....>>>>>>>>.>>>>>......<<..
......<<<<<.....<...<<<<<<<.<<<<<....<<<<<......>>
>>>.....>>>>>...<<<<<<<<<.<<<....>>>>>>>>>>>>....<
<..<<<....>>>>>.>>>>>>>..>...>>>>>.<<<....<<<..<<<
<<<<<.......>>>>>>>>>>>......>>>..<<<<<<<<....>>>>
...>>>>.>>.<<<<<............>>>>>.<<<<....>>>>...>
>>>>>.........<<<....<<<<....>>>>..>>>..>>..>>>>..
.<<<<<<<<...>>>>>>>>...<<<<<<<<.......>>>>>>>>....
.<<<<<((.....<<<<<.....<<..))>>.......>>>>>>>>>>..
>>>>>>>>>..........<<<((......<<....<<<.<<<<<<<.<<
<<<<<<<.....<<<<<<<<.....>>>>>>>>....>>>>>>>..>>>>
>>>>>...<<<<<<.....<<<<<<<.<..<<<<<<<<<..<<<......
>>>.....>>>>>>>>>..>........<<....>>.>>>>>>>....>>
>.>>>...>>>....>>....<<<<<<<...<<...<<<<.........>
>>>...>>>>>>>>>.........<<<<<<..<<<<<<<<<<<<<<....
.>>>>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<.....
.<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<..<<.<<<<
<<..<<<<<<<<<.......<<........>>..........<<<<<<<.
..<<<<........<<<.<<<.......>>>.>>>......>>>>...<<
.<<<..<<<<<<<<<....<<<<<<.<<....>>...<<<<......>>>
>..>>>>>>....<<<<<.<<<<<<<.........<<<<<<....>>>>>
>.......>>>>>>>.....<<<<<.....>>>>>........>>>>>..
..>>>.>>>...>>>>>>>>....>>>>>>>....>.>>>>>>>>.....
<<<<<<<.....<<<..<<..<<<......>>>..>>....>>>.....>
>>>>>>......<....<<<<<<<........>>>>>>>....>.....>
>>>>>.....<<<<<<.........>>>>>>.......>>...>>>>>>>
>>>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<<<<<..<<<<<<<
<<<<<....>>>>>>>>>>>>..>>>>>>>>>>>>>..>>>.>>>>..>.
>>...>.....<.<<<<<<<....>>>>>>>.>............
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)		G3 K4 K5 A6 N8 G9 R14 K15 K19 R20 F23 R24 W25 S26 D27 R29 K31 R33 R36 L37 P48 Q49 R51 Q64 N66 S67 R70 K71 R74 I78 K79 G90 D91 G92 E106 G107 I108 G110 P111 K112 G113 G114 S115 M116 D118 R123 K128 R131 S133 E136 K139 G140 R141 K142
Binding residue
(residue number reindexed from 1)		G1 K2 K3 A4 N6 G7 R12 K13 K17 R18 F21 R22 W23 S24 D25 R27 K29 R31 R34 L35 P46 Q47 R49 Q62 N64 S65 R68 K69 R72 I76 K77 G88 D89 G90 E104 G105 I106 G108 P109 K110 G111 G112 S113 M114 D116 R121 K126 R129 S131 E134 K137 G138 R139 K140
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Mar 7 08:59:27 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 = 'BN', 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='BN', 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 = '0003735,0005840,0006412,0015935', uniprot = '', pdbid = '4v4n', asym_id = 'BN'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0015935', uniprot='', pdbid='4v4n', asym_id='BN')
    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>