Structure of PDB 4d5y Chain L Binding Site BS01

Receptor Information
>4d5y Chain L (length=199) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRP
IVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKST
ESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPV
RNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQD
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)		L10 K11 H13 F14 H15 K16 W18 Q19 W25 N27 P29 A30 R31 K32 I33 R34 R35 K37 R39 K42 S52 P54 R56 V59 R60 C61 P62 T63 V64 Y66 H67 K69 R71 R74 K88 R92 D99 R101 R102 K105 E108 Q111 Q115 R129 Q149 L150 P156 V157 V160 Y161 K163 E164 K165 F179 R183 R186 R190 R195 K197 R198
Binding residue
(residue number reindexed from 1)		L3 K4 H6 F7 H8 K9 W11 Q12 W18 N20 P22 A23 R24 K25 I26 R27 R28 K30 R32 K35 S45 P47 R49 V52 R53 C54 P55 T56 V57 Y59 H60 K62 R64 R67 K81 R85 D92 R94 R95 K98 E101 Q104 Q108 R122 Q142 L143 P149 V150 V153 Y154 K156 E157 K158 F172 R176 R179 R183 R188 K190 R191
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sun Mar 2 03:43:52 2025

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 = 'L', 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='L', 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', uniprot = '', pdbid = '4d5y', asym_id = 'L'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4d5y', asym_id='L')
    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>