Structure of PDB 4d67 Chain X Binding Site BS01

Receptor Information
>4d67 Chain X (length=119) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAM
KKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAY
VRLAPDYDALDVANKIGII
Ligand information
>4d67 Chain 2 (length=3616) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggccggcg
cgcgcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguca
acaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaag
agggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcc
cggaggauucaacccggcggcggguccggccgugucggcggcccggcgga
ucuuucccgcgcgggggaccgucccccggaccggcgaccggccgccgccg
ggcgcauuuccaggcggugcgccgcgaccggcuccgggacggcugggaag
gcccggcggggaagguggcucgggggcccccgaguguuacagcccccccg
gcagcagcacucgccgaaucccggggccgagggagcgagacccgucgccg
cgcucuccccccucccggccccccggggggggccgggccaccccucccac
ggcgcgaccgcucucccaccccuccucccgggucggggggcggggcggac
uguccccagugcgccccgggcgggucgcgccgucgggcccgggggagguu
cucucggggccacgcgcgcgucccccgggggacggcggagcgagcgcacg
gggucggcggcgacgucggcuacccacccgacccgucuugaaacacggac
caaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgu
ggcgcaaugaaggugaaggccggcgcgcucgccggccgaggugggauccc
gaggccucuccaguccgccgaggggcaccaccggcccgucucgcccgccg
cgccggggagguggagcacgagcgcacguguuaggacccgaaagauggug
aacuaugccugggcagggcgaagccagaggaaacucugguggagguccgu
agcgguccugacgugcaaaucggucguccgaccuggguauaggggcgaaa
gacuaaucgaaccaucuaguagcugguucccuccgaaguuucccucagga
uagcuggcgcuccaguuuuauccgguaaagcgaaugauuagaggucuugg
ggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagccc
ggcucgcuggcguggagccgggguggaaugcgagugccuagugggccacu
uuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaagg
cgcccgaugccgacgcucaucagaccccagaaaagguguugguugauaua
gacagcacugccgaaucaacuagcccugaaaauggauggcgcuggagcgu
cgggcccauacccggccgucgccggcgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggaggccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggugcagccgacuuagaacuggugcggaccaggggaauccg
acuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacg
cgaugugauuucugcccagugcucugaaugucaaagugaagaaauucaau
gaagcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggaugaacgagauucc
cacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuu
ggcggaaucagcggggaaagaagacccuguugagcuugacucuagucugg
cacggugaagagacaugagagguguagaauaagugggaggcccgggccgc
cggugaaauaccacuacucugaucguuuuuucacugacccggugaggcgg
gggggcgagcccgaggggcucucgcuucuggcgccaagcgcccgcccggc
cgggcgcgacccgcuccggggacagugccagguggggaguuugacugggg
cgguacaccugucaaacgguaacgcagguguccuaaggcgagcucaggga
ggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuuga
uuuucaguacgaauacagaccgugaaagcggggccucacgauccuucuga
ccuuuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaac
uggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucg
augucggcucuuccuaucauugugaagcagaauucgccaagcguuggauu
guucacccacuaauagggaacgugagcuggguuuagaccgucgugagaca
gguuaguuuuacccuacugaugauguguuguugccaugguaauccugcuc
aguacgagaggaaccgcagguucagacauuugguguaugugcuuggcuga
ggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccuc
uaagucagaaucccgcccaggcgaacgauacggcagcgccgcggagccuc
gguuggccucggauagccggucccccgccuguccccgccggcgccgcgcg
ccgggaccgggguccggugcggagugcccuucguccugggaaacggggcg
cggccggaaaggcggccgcccccucgcccgucacgcaccgcacguucgug
gggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggggu
uucguacguagcagagcagcucccucgcugcgaucuauugaaagucagcc
cucgacacaaggguuu
.........................<<<<<<.....<<....>>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..[[[..<.......<..<<....<.....>....>>..>....
...>..<<<<<<<<.......<<.<<<.<<<.......<<<<.....<<<
<......>>>>.....((......<<<.....))>>>.....>>>>>>>>
>>>>....>>>>>>>>.......<<<<<<<........>>>>>>>.....
(((((..<<<<<<)))))..]]]...........................
.......<<....>>................<.......>..........
..........................<<<<<<<<..<<<......<<<<<
.<<<<.........<<<<<<<......<<<<..<<<<.<<<.<<<<.<<<
<.<<<<<<<<>>>>>>>>..>>>>.>>>>.>>>.>>>>.>>>>>>>>>>>
.......>>>>.>>>>>..<<<<<.<<..<<<<<<<.<..<<<.<.....
....<<.<<<.....<<.<<<<<<<..>>>>>>>...>>....>>>.>>.
..........>.>>>.....>>>>>>>>..............<<.<<<..
<<<<.....<<....<<<<<<<<<..>>>>>>>>>...<.<<<<<.<<<<
<<<<<<<<<<.<........<<<.<.<<..>>..>>>>...<<<<<<.<<
<......>>>.>>>>>>.>.>.>>>>>>>>>>>.>>....>>>>>.>...
......>>......<<<.<<<<<<<..>>>>>>>>>>.>>>>.>>>..>>
...>>..>>>>>....>>>...>>>>>>>>..<<<<........>>>><<
<<<<....<<<<<<<<<<<<<..<<<...<<<<........>>>>.....
>>>...<<....>>...<<<<<<<<....>>>>>>>>..<<<<<..<<<<
..<<<...........>>>..>>>>..>>>>>.<<<<<<<<<.<<<....
....>>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<...<<<<<<.
....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>..
.<<<..<<.<<........>>>>.>>>....>>>>>>>>>...<<.....
..>>......>>>>>>......>.>>..<<<<<<......<<<....>>>
..<<.<<<<<<.<<.<<<<<<<<....<<<....<<<....<<<..<<<<
.<.........>.>>>>>>>....>>>..>.>>....>>>>>>....<<<
<<<<<.........>>>>>>>>....>>>>..>>>>>>..>>..<<<<.<
<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<
<(((.......<<<<<......<..........<<<.<<<<<<<<<....
....<<...>>....>>>>>>>>>>>>..........))).>....>>>>
>..>>>...>>>>>>><<<<<<.<...>.>>>>>>....>>>>>>...<<
<<<<<..<<......<<<<.<<<<....>>>>>>>>....>>.>>>>>>>
........>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<
<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<
<<<<...<<....<<<....>>>..........<<.<<<<<<<<<...>>
>>>>>>>>>......>>....>>...<<<<<........>>>>>))<<<<
..<<.......<<<<<<<<....>>>>>>>>..<<<....>>>......<
<<<<<<...<<<<<<<<<<<<<<<<<<<<<<<..{{{..>>>>>>.....
<<<<..<<<.<<<<.....<<<.....>>>.....>>>>>>>...>>>>.
.....<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>>.....
....>>>>>>>................>>..>>>>>>>>..>>.....<<
......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<
<<.<<...............<<<<<...............>>>>><<.<<
<<<<<<<<......>>>>..>>>>>>.>>............<<<<<<<<<
..<<<.........>>>..<<<<<<<....<<<<.....>>>>......>
>>>>>>...<<..<<<..<<<<<<....<<<.....<<<<....>>>>..
...>>>.>>>>..>>>>>.<<<<.........>>>>.........<....
.......<<<<<.......>>>>>.....>.....>>....>>.>>>>>>
>.....>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>
>>....[[[[[..{{{.{{......[[[[.{.[[[[..<<<<<.<<<<<<
<<<.<<<<<..<<<.<.<<<<..........<<<<<..<<<<..>>>>..
..........>>>>>.>>>>.>..>>>..>>>>>...<<<<<......<<
<.....<<<.<.....>.>>>................<<<<<<<......
>>>>>>>..>>>...>>>>>....>>>>>>>>>..>>>>>....<<....
.>>...<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<
<<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<..<
<<<.......>>>>..>>>.<<<....>>>.>>)))]......((((((.
.(((..>>>>>>.)))))))))..........]]]]...}]]]]......
.<<.<...<<<<<<...<<.......>>...>>>>>>....>.>.>....
...<<<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<...
......>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.
>>>>....}}..}}}.]]]]].....<<<<<<....<<<....<<<<<..
...............>>>>>..<<<<....<<<<....<<.<<<<<<.}}
}..>>>>..>>.>>...>>>>...>>>>.<<<<...<<<<<.........
..>>>>>...>>>>..>>>....>>>>>>.....<<<<<<<.<<..<<<.
<...<<<.........<<<<.<<<....<<.....<<<<<<..>>>.>>>
..>>.....>>>.>>>>........>>>...<<<..<<<.....<<<<.<
<<<<<<......>>>>>>>>>>>....>>>..>>>.............>.
>>>..>>>>>>>>>.<<<<.....................<.<<<<<<<.
<<.....<<<<....<<<<<......>>>>>...>>>>....>>....>>
>>.>>>.>..>>.>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4d67 Cryo-Em Structures of Ribosomal 80S Complexes with Termination Factors and Cricket Paralysis Virus Ires Reveal the Ires in the Translocated State
Resolution9.0 Å
Binding residue
(original residue number in PDB)
K38 T45 R47 R48 K50 T51 R53 L54 R55 R56 Q57 P58 K59 Y60 T83 S85 K89 N93 N105 K106 N125 T126 L127 P130 K135 Y137 R139
Binding residue
(residue number reindexed from 1)
K1 T8 R10 R11 K13 T14 R16 L17 R18 R19 Q20 P21 K22 Y23 T46 S48 K52 N56 N68 K69 N88 T89 L90 P93 K98 Y100 R102
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Nov 15 15:23:52 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 = '4d67', asym_id = 'X', bs = 'BS01', title = 'Cryo-Em Structures of Ribosomal 80S Complexes wi...s Ires Reveal the Ires in the Translocated State '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4d67', asym_id='X', bs='BS01', title='Cryo-Em Structures of Ribosomal 80S Complexes wi...s Ires Reveal the Ires in the Translocated State ')
   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 = '0003735,0005840,0006412,0019843', uniprot = '', pdbid = '4d67', asym_id = 'X'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0019843', uniprot='', pdbid='4d67', asym_id='X')
    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>