Structure of PDB 3j7q Chain o Binding Site BS01

Receptor Information
>3j7q Chain o (length=104) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQ
TKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKG
QVIQ
Ligand information
>3j7q Chain 5 (length=3662) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucggccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccucccggcgccgccggggggggccgggccaccc
cucccacggcgcgaccgcucggggcggacuguccccagugcgccccgggc
gggucgcgccgucgggcccgggggaggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcacacgcag
uuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucuc
aaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcguga
gccgggcguggaauggagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagcggcgggggcggcgcgcgcg
cgcgcccgcccccggagccccgcggacgcuacgccgcgacgaguaggagg
gccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgc
cgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuug
aaggccgaaguggagaaggguuccaugugaacagcaguugaacauggguc
agucgguccugagagaugggcgagcgccguuccgaagggacgggcgaugg
ccuccguugcccucggccgaucgaaagggagucggguucagauccccgaa
uccggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcga
ccgaucccggagaagccggcgggagccccggggagaguucucuuuucuuu
gugaagggcagggcgcccuggaauggguucgccccgagagaggggcccgu
gccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggc
ccuugaaaauccgggggagaggguguaaaucucgcgccgggccguaccca
uauccgcagcaggucuccaaggugaacagccucuggcauguuggaacaau
guagguaagggaagucggcaagccggauccguaacuucgggauaaggauu
ggcucuaagggcugggucggucgucggccggcgccuagcagccgacuuag
aacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucg
cgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggaugaacgagauucccacugucccuaccuacuauccagcg
aaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaagac
ccuguugagcuugacucuagucuggcacggugaagagacauguuuuuuca
cugacccggugaggcgggggggcgagccccgaggggcucucgcuucuggc
gccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacag
ugccagguggggaguuugacuggggcgguacaccugucaaacgguaacgc
agguguccuaaggcgagcucagggaggacagaaaccucccguggagcaga
agggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccguga
aagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucau
agcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauuguga
agcagaauucaccaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaug
uguuguugccaugguaauccugcucaguacgagaggaaccgcagguucag
acauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccau
cugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgga
acgauacggcagcgccgcggagccucgguuggccucggauagccgguccc
ccgcgggguccggugcggagugcccuucguccugggaaacggggcgcggc
cggagaggcggccgcccccucgcccgucacgcacgccguucguggggaac
cuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgua
cguagcagagcagcucccucgcugcgaucuauugaaagucagcccucgac
acaaggguuugu
..........................<<<<<.....<......>......
>>>>>...........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<..<<<<<...<<<<<<<<<<<...>>>>>>>.>>>>...
..>>>>>..<<<<<<<<<....<<<<<<<<........<<<<<<<.....
<<<<......>>>>.....((......<<<.....))>>>.....>>>>>
>>...>>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..(((((.>>>>>..>>>..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<..
.....<<<<<<<.<<<.....<<<<<<<<<<<...<<<....<<<<<.<<
....<<<<.<<<..<<<<<>>>>>>>>>>>>>>>>.>>>......>>>.>
>>>>>>>>>>......>>>.>>>.>>>>...<<<<<<<..<<<<<<<<<.
.<<<....<...<<.<<<.<<<<...<<.<<<<<..>>>>>>.>....>>
>>.>>>>>.........>.>>>....>>>>>>>>>...............
......<<<<..<<<<<<...<<<<<.>>>>>.>>>>>>....<<<.<<<
<.<<<<<<<<<<<<<<<<<<<<<<<<.<<<<....>>>>.>>>>>>>>>>
>.>>>>>>>>>>.>>>...>.>>>...>>>........<<<<<<<<....
.>>>>>>>>........>>>>........>>.>>>>>....>>>...>>>
>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<
<...<<<<........>>>>.....>>>...<<....>>...<<<<<<<<
....>>>>>>>>..<<<<<...<<<..<<<...(((..[[.>>>..>>>.
...>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>
>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<
<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.
>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.
>>..<<<<<<......<<<....>>>..<<.<<<<<<<............
<<<<<<<<<...<<<....<<<....<<<..<.<<<<.<.....>.>>>>
>.>>>....>>>..>.>>...>>>>>>>...<<<<<<<<<........>>
>>>>>>>...>>...>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>
>>>....<<<......>>>...<<<<<<<...<<<(((.......<<<<<
.....<<..........<<<.<<<<<<<<<<.......<<<<<.<<....
<<.........>>....>>.........<<......>>...>>>>>...>
>>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>>>>>
><<<<<<.<<<..........]]..)))......................
.<<<..>>>.......................>>>>>>>>>....>>>>>
>.<.<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>
>>>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>>
>>.<<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>...
.((<<<<<<...<<....<<<....>>>..........<<.<<<<<<<<<
...>>>>>>>>>>>......>>....>>...<<<<<........>>>>>)
)<<<<....<<<<...<<<<<<<<....>>>>>>>>..<<<....>>>..
.<..<<<<<<<...<<<<<<<<<<<<<<<<<<<<<<<..[[[..>>>>>>
....<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..
>>>>>.....<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>>
.........>>>>>>>..>............>>>>.>>>>>>>>..>>..
...<<......>>>>>>>.<<<<.....>>>>.>>>>....<<<<.....
<<<<<<<.<<.........<.....<<<<<....<....>.....>>>>>
<<.<<<<<.<<<<<...<<<<<<.>>>>>>........>>>>>...>>>>
>.>>............<<<<<<<<<..<<<.........>>>..<<<<<<
<....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<.
.....<.....<<<<....>>>>.....>...>>>>..>>>>><<<<<<.
......>>>>>>........<...........<<<<<.......>>>>>.
....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>.
...>>....<<<<<........>>>>>....<<<<<..<<<.<<......
<<<<.<<<<<<..<<<<..<<<<<<<<<.<<<<<<<<<<..>>>>>>>>>
>...<<<<<.....<<<<..<<.<<<<<<....>>>>>>>>.........
.....<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>....>
>>>>>>>>...>>>>...<<<.....>>>..<<<<<<...........>>
>>>>..<<...<<<<<<....<<<<<<.......>>>>>>.....<<.[.
(((>>.....>>>>>>...<<<..<<<<.......>>>>..>>>.<<<..
..>>>.>>)))].....<<<<<<<..<<<...))))).>>>>>>>>>>..
.......>>>>..>>>>>>.......<<.<...<<<<<<...<<......
.>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<.<.<<<<
<......>>>>>...>.>.<<<.........>>>.....>>>>>..>...
>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>....
.<<<<<<.<..<<<..<.<<<<<.................>>>>>.><<<
<....<<<<...<<<.<<<<<<.]]]..>>>>..>>.>>>..>>>>...>
>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>...>.>
>>>>>.....<<<<<<<.<<..<<<.....<<.........<<<<<..<<
<<..>>>>.>>>>>........>>....<<..<<<<....<<<<.<<<<<
<<......>>>>>>>>>>>...>>>>..>>..............>>>..>
>>>>>>>><<<<<.<.............>....<<.<<<<<<<.<<....
.<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>
.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3j7q Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.
Resolution3.4 Å
Binding residue
(original residue number in PDB)
V2 N3 P5 R8 R9 T10 F11 K13 G16 K17 H18 Y26 K28 G29 D31 S32 Y34 A35 Q36 G37 R39 R40 R43 K44 G47 Y48 G50 Q51 T52 K53 P54 I55 F56 K58 A60 K61 K64 K65 V67 S79 K80 R81 M82 A84 K86 K89 K97 K98
Binding residue
(residue number reindexed from 1)
V1 N2 P4 R7 R8 T9 F10 K12 G15 K16 H17 Y25 K27 G28 D30 S31 Y33 A34 Q35 G36 R38 R39 R42 K43 G46 Y47 G49 Q50 T51 K52 P53 I54 F55 K57 A59 K60 K63 K64 V66 S78 K79 R80 M81 A83 K85 K88 K96 K97
Gene Ontology
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UnboundLocalError
Python 3.6.8: /usr/bin/python3
Sat Nov 16 18:00:23 2024

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 = '3j7q', asym_id = 'o', 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='3j7q', asym_id='o', 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 = '3j7q', asym_id = 'o'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='3j7q', asym_id='o')
    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>