Structure of PDB 4d5y Chain M Binding Site BS01

Receptor Information
>4d5y Chain M (length=139) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMP
FKCMQLTDFILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERK
AKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALLKASP
Ligand information
>4d5y 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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PDB4d5y 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)		V2 R4 N34 R35 K53 P65 H66 K71 R90 W91 K94 A97 R98 K101 M113 K114 K116 K117 M118 N120 R121 K128 K129 K132
Binding residue
(residue number reindexed from 1)		V1 R3 N33 R34 K52 P64 H65 K70 R89 W90 K93 A96 R97 K100 M112 K113 K115 K116 M117 N119 R120 K127 K128 K131
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 23:32:23 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 = '4d5y', asym_id = 'M', 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='4d5y', asym_id='M', 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 = '0003723,0003735,0005840,0006412', uniprot = '', pdbid = '4d5y', asym_id = 'M'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003723,0003735,0005840,0006412', uniprot='', pdbid='4d5y', asym_id='M')
    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>