Structure of PDB 4v4n Chain BQ Binding Site BS01

Receptor Information

>4v4n Chain BQ (length=158) Species: 2190 (Methanocaldococcus jannaschii)

MARMHARKRGKSGSKRPPRTAPPIWVEYTVEEIENLVVKLRKEGYSTAMI
GTILRDQYGIPSVKLFKDPDNPNRNLTITRILEKHGLAPEIPEDLMFLIR
RAVNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKNWRYDP
ETAKLLVR

Ligand information

>4v4n Chain B2 (length=1495)

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

Structure summary

• PDB: 4v4n Structure of the SecY channel during initiation of protein translocation.
• Resolution: 9.0 Å
• Binding residue (original residue number in PDB): M1 A2 R3 H5 A6 R7 K8 R9 G10 K11 S12 K15 R16 P17 A48 M49 G51 T52 R55 S62 V63 K64 R74 N75 T77 T79 D94 R101 H108 H112 D115 L116 H117 R120 Q123 S127 K128 R131 K134 Y135 Y136 K139 K141
• Binding residue (residue number reindexed from 1): M1 A2 R3 H5 A6 R7 K8 R9 G10 K11 S12 K15 R16 P17 A48 M49 G51 T52 R55 S62 V63 K64 R74 N75 T77 T79 D94 R101 H108 H112 D115 L116 H117 R120 Q123 S127 K128 R131 K134 Y135 Y136 K139 K141

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Mar 7 08:56:20 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 = 'BQ', 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='BQ', 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 = 'BQ'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v4n', asym_id='BQ')

    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>