Structure of PDB 3jah Chain P Binding Site BS02

Receptor Information
>3jah Chain P (length=153) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKE
Ligand information
>3jah 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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PDB3jah Structural basis for stop codon recognition in eukaryotes.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		R3 Y4 R18 S20 R23 H25 F26 K27 R30 Q34 K37 K55 R62 Y63 N64 G65 G66 G68 R69 A71 Q72 K74 Q80 R82 W83 P84 K85 K86 N97 S100 N101 L104 Q118 V119 K121 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 P138 Y139 M140 S141
Binding residue
(residue number reindexed from 1)		R2 Y3 R17 S19 R22 H24 F25 K26 R29 Q33 K36 K54 R61 Y62 N63 G64 G65 G67 R68 A70 Q71 K73 Q79 R81 W82 P83 K84 K85 N96 S99 N100 L103 Q117 V118 K120 R126 T128 Y129 R130 A131 H132 G133 R134 I135 N136 P137 Y138 M139 S140
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 22:57:46 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 = '3jah', asym_id = 'P', bs = 'BS02', title = 'Structural basis for stop codon recognition in eukaryotes.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3jah', asym_id='P', bs='BS02', title='Structural basis for stop codon recognition in eukaryotes.')
   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 = '0003735,0005840,0006412,0015934', uniprot = '', pdbid = '3jah', asym_id = 'P'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0015934', uniprot='', pdbid='3jah', asym_id='P')
    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>