Structure of PDB 3jaj Chain r Binding Site BS01

Receptor Information
>3jaj Chain r (length=125) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHHKTVGV
EPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNK
YRPDLRMAAIRRASAILRSQKPVMV
Ligand information
>3jaj Chain 5 (length=3658) [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
cguagcagagcagcucgcugcgaucuauugaaagucagcccucgacacaa
ggguuugu
..........................<<<<<.....<......>......
>>>>>...........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<..<<<<<...<<<<<<<<<<<...>>>>>>>.>>>>...
..>>>>>..<<<<<<<<<....<<<<<<<<........<<<<<<<.....
<<<<......>>>>.....((......<<<.....))>>>.....>>>>>
>>...>>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..(((((.>>>>>..>>>..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<..
.....<<<<<<<.<<<.....<<<<<<<<<<<...<<<....<<<<<.<<
....<<<<.<<<..<<<<<>>>>>>>>>>>>>>>>.>>>......>>>.>
>>>>>>>>>>......>>>.>>>.>>>>...<<<<<<<..<<<<<<<<<.
.<<<....<...<<.<<<.<<<<...<..<<<<<..>>>>>..>....>>
>>.>>>>>.........>.>>>....>>>>>>>>>...............
......<<<<..<<<<<<...<<<<<.>>>>>.>>>>>>....<<<.<<<
<.<<<<<<<<<<<<<<<<<<<<<<<<.<<<<....>>>>.>>>>>>>>>>
.>>>>>>>>>>>.>>>...>.>>>...>>>........<<<<<<<<....
.>>>>>>>>........>>>>........>>.>>>>>....>>>...>>>
>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<
<...<<<<........>>>>.....>>>...<<....>>...<<<<<<<<
....>>>>>>>>..<<<<<...<<<..<<<...(((..[[.>>>..>>>.
...>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>
>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<
<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.
>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.
>>..<<<<<<......<<<....>>><.<<<<<<<<<<............
<<<<<<<<<...<<<....<<<....<<<..<.<<<<.<.....>.>>>>
>.>>>....>>>..>.>>...>>>>>>>...<<<<<<<<<........>>
>>>>>>>...>>...>>>>>>>.>>>>.<<<<.<<<<<.....>>>>>.>
>>>....<<<......>>>...<<<<<<<...<<<(((.......<<<<<
.....<<..........<<<..<<<<<<<<<.....<.<<<<<.<<....
<<.........>>....>>.........<<......>>...>>>>>.>.>
>>>>>>>>.>>>..........))).>>...>>>>>..>>>...>>>>>>
><<<<<<.<<<..........]]..)))......................
.<<<..>>>.......................>>>>>>>>>....>>>>>
>...<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>
>>>>>........>>>>>><<.....<<.....<<<<<<.......>>>>
>>.<<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>...
.((<<<<<<...<<....<<<....>>>..........<<.<<<<<<<<<
...>>>>>>>>>>>......>>....>>>..<<<<<........>>>>>)
)<<<<....<<<<...<<<<<<<<....>>>>>>>>..<<<....>>>..
.<..<<<<<<<...<<<<<<<<<<<<<<<<<<<<<<...[[[...>>>>>
....<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..
>>>>>.....<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>>
.........>>>>>>>..>..........>..>>>.>>>>.>>>..>>..
...<<......>>>>>>>.<<<<.....>>>>.>>>>....<<<<.....
<<<<<<<.<<.........<.....<<<<<.....<..>......>>>>>
<<.<<<<<.<<<<<...<<<<<<.>>>>>>........>>>>>...>>>>
>.>>............<<<<<<<<<..<<<.........>>>..<<<<<<
<....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<.
<....<.....<<<<....>>>>.....>..>>>>>..>>>>><<<<<<.
......>>>>>>........<...........<<<<<.......>>>>>.
....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>.
...>>....<<<<<........>>>>>....<<<<<..<<<.<<......
<<<<.<<<<<<..<<<<..<<<<<<<<<.<<<<<<<<<<..>>>>>>>>>
>...<<<<<.....<<<<..<<.<<<<<<....>>>>>>>>.........
.....<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>....>
>>>>>>>>...>>>>...<<<.....>>>..<<<<<<...........>>
>>>>..<<...<<<<<<....<<<<<<.......>>>>>>.....<..[.
(((.>.....>>>>>>...<<<..<<<<.......>>>>..>>>.<<<..
..>>>.>>)))]......<<<<<<..<<<...))))).>>>>>>>>>...
.......>>>>..>>>>>>.......<<.<...<<<<<<...<<......
.>>...>>>>>>....>.>.>.......<.<<<.<<<<<<..<.<.<<<<
........>>>>...>.>.<<<.........>>>.....>>>>>..>...
>>>..>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>....
.<<<<<<.<..<<<..<.<<<<<.................>>>>>.><<<
<....<<<<...<<<.<<<<<<.]]]..>>>>..>>.>>>..>>>>...>
>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>...>.>
>>>>>.....<<<<<<<.<<..<<<.....<<.........<<<<<..<<
<<..>>>>.>>>>>........>>....<<..<<<<....<<<<.<<<<<
<<......>>>>>>>>>>>...>>>>..>>..............>>>..>
>>>>>>>><<<<<.<.............>....<<.<<<<<<<.<<....
.<<<<....<<<<<..>>>>>...>>>>....>>....>>>>.>>>.>>.
.>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3jaj Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.
Resolution3.75 Å
Binding residue
(original residue number in PDB)
R11 N12 S15 K19 R20 K22 T24 R35 N36 S37 F38 R39 Y40 H46 K47 R66 R67 S68 T81 K84 N85 S92 R94 H95 M96 R98 K99 N100 R107 M108 R112
Binding residue
(residue number reindexed from 1)
R10 N11 S14 K18 R19 K21 T23 R34 N35 S36 F37 R38 Y39 H45 K46 R65 R66 S67 T80 K83 N84 S91 R93 H94 M95 R97 K98 N99 R106 M107 R111
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Nov 15 11:50:10 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 = '3jaj', asym_id = 'r', bs = 'BS01', title = 'Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3jaj', asym_id='r', bs='BS01', title='Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.')
   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 = '3jaj', asym_id = 'r'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='3jaj', asym_id='r')
    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>