Structure of PDB 4v4n Chain BO Binding Site BS01

Receptor Information
>4v4n Chain BO (length=148) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MANFRHIVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMK
AGYLTDEQVKKIEEILADPVAHGIPRWAVNRPKDYETGRDLHLITAKLDM
AIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQTVGVSRKKK
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)		Q20 W23 T26 K29 G30 I31 G32 N34 F48 K50 W77 A78 N80 R81 P82 K83 E86 L98 I102 D105 R108 Y115 R116 R119 H120 L124 P125 V126 R127 G128 Q129 R130 T131 R132 S133 N134 F135 R136 R137 Q139 T140 G142 V143 R145 K146 K148
Binding residue
(residue number reindexed from 1)		Q20 W23 T26 K29 G30 I31 G32 N34 F48 K50 W77 A78 N80 R81 P82 K83 E86 L98 I102 D105 R108 Y115 R116 R119 H120 L124 P125 V126 R127 G128 Q129 R130 T131 R132 S133 N134 F135 R136 R137 Q139 T140 G142 V143 R145 K146 K148
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Mar 7 09:14:05 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 = 'BO', 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='BO', 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 = '0003676,0003723,0003735,0005840,0006412', uniprot = '', pdbid = '4v4n', asym_id = 'BO'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003676,0003723,0003735,0005840,0006412', uniprot='', pdbid='4v4n', asym_id='BO')
    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>