Structure of PDB 3j7r Chain SW Binding Site BS01

Receptor Information

>3j7r Chain SW (length=129) Species: 9823 (Sus scrofa)

VRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFE
IIDDHRAGKIVVNLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSRQFGF
IVLTTSAGIMDHEEARRKHTGGKILGFFF

Ligand information

>3j7r Chain S2 (length=1742)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgccgcc
ucucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaa
gcaggcccgagccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcgguc
ggcgucccccaacuucuuagagggacaaguggcguucagccacccgagau
ugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgc
gcuacacugacuggcucagcgugugccuacccuacgccggcaggcgcggg
uaacccguugaaccccauucgugauggggaucggggauugcaauuauucc
ccaugaacgaggaauucccaguaagugcgggucauaagcuugcguugauu
aagucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugg
uuuagugaggcccucggaucggccccgccggggucggcccacggcccugg
cggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagu
cguaacaagguuuccguaggugaaccugcggaaggaucauua

...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<...<<<..........>>>..>>.>>......<<...
.....<<<.<....<<....<<<<<..................<<.....
<<.............>>......>>.........<<<<...<<<<<<...
.>>>>>>...>>>>....<<<<<...<......>..>>>>>.........
..<<<<.<<<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>...<
<....>>.....>>>>>>.........<<<....<<<.....>>>..>>>
..>...>>.>.....<<<<<<.<..<<<....>>>..>..>>>.>>>...
...<<..<...........>..>>.........<<<<<((......<<<<
.........)).........>>>>.>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<.<<.....<<.<.<<....>>.>.>><<.
<..<...........>>.>>..<<<<<<.<.......<<...<.......
>.<<<<.......>>>>...>>......>.>>>..>>>.......<<...
.<<<<<<<...............>>>>>>>...>>....>>....<<<<<
<..<...<<<<..<<<.<<<<<<<<...<<<......>>>......>>>>
>>>>.>>>.......<<....>>...>>>>..>..>>>.>>>...>>>..
.>>.>....<<<<<<....<...<<<<.<.....>.>>>>...>.>>>>>
>..........<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>
>>.>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<
<....>>>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..
<<<.<<<<........<<........>>..........<<<<<......<
<<<<........<...<<........>>...>......>>>>>...<<.<
<<....<<<<<<<....<<<.<<<<......>>....<<......>>...
.>>.>>>....<<<...<...<<<<..<<<.....<<<...<<<....>>
>..>>>.....>>>..>>>>..>.....<<<<<.....>>>>>.......
.>>>....>>>.>>>...>...>>>>>.......>>>>>......>>>>.
>>>.....<<.<<<........<.......<<<.<<<<....>>>>.>>>
....>.........>>>.>>.........<..<<<<<..........>>>
>>.>.........>>>>>.....<<<<<<<<.......>>>>>>>>....
..>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<
<<.<<<..<<<<.<<...<<<<<.<<<<<<<<<<<<.....>>>>>>>>>
>>>...>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.
>>...>.....<<<<<<<<<....>>>>>>>>>.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j7r Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): V2 R3 M4 V6 A8 D9 K12 S13 N16 R20 K22 R28 K32 R57 A58 K60 K71 I75 S76 R78 D80 Q82 K88 W89 T105 T106 S107 G109 H120 G122 K124 F130
• Binding residue (residue number reindexed from 1): V1 R2 M3 V5 A7 D8 K11 S12 N15 R19 K21 R27 K31 R56 A57 K59 K70 I74 S75 R77 D79 Q81 K87 W88 T104 T105 S106 G108 H119 G121 K123 F129

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Feb 27 14:07:23 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 = '3j7r', asym_id = 'SW', bs = 'BS01', title = 'Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3j7r', asym_id='SW', bs='BS01', title='Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.')

   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 = '3j7r', asym_id = 'SW'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='3j7r', asym_id='SW')

    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>