Structure of PDB 4v4n Chain BD Binding Site BS01

Receptor Information

>4v4n Chain BD (length=172) Species: 2190 (Methanocaldococcus jannaschii)

KKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRL
LAARGKQAEIEREQLLARLKRLGLLPEDAVLDDVLSLTIEDILERRLQTI
VYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTS
PFANPQHPERMMIEKAKQGGEA

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): K9 K10 Y11 P15 H16 W18 R27 V28 M30 D31 K36 N37 K38 K39 W42 K43 R52 R53 R54 R56 E69 Q72 R76 R79 R116 R119 Q120 R122 V126 H127 Q135 I136 R138 S139 P140 R156 S158 H165 P166 E167 K173
• Binding residue (residue number reindexed from 1): K1 K2 Y3 P7 H8 W10 R19 V20 M22 D23 K28 N29 K30 K31 W34 K35 R44 R45 R46 R48 E61 Q64 R68 R71 R108 R111 Q112 R114 V118 H119 Q127 I128 R130 S131 P132 R148 S150 H157 P158 E159 K165

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Mar 7 08:55:40 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 = 'BD', 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='BD', 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 = '0003723,0003735,0006412,0015935,0019843', uniprot = '', pdbid = '4v4n', asym_id = 'BD'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003723,0003735,0006412,0015935,0019843', uniprot='', pdbid='4v4n', asym_id='BD')

    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>