Structure of PDB 7oyd Chain S Binding Site BS01

Receptor Information
>7oyd Chain S (length=176) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKASGTLREYKVVGRCLPTPKCRTPPLYRMRIFAPNHVVAKSRFWYFVSQ
LKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDL
TTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKI
KFPLPHRVLRRQHKPRFTTKRPNTFF
Ligand information
>7oyd Chain 5 (length=3358) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacccggcgccggggggcccaaguccuucugau
cgaggccgcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggaucaacccggcggcggccggccgugccggggggcggaucuggaccg
ccccccggccggcgaccggccgccgccgggcgcauuuccaccgggcggug
cgccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggc
ccggccggguguuacagcccgcccccggcagcagcgacucgccgaauccc
ggggccgagggagcgagacccgugccgccgcgcucuccccccuggggggg
ccgggccaccccucccacggcgcgaccgcggggcggacuguccagugcgc
cccgggcgggucgcgccgucgggcccggggggccacgcgcgagcgcacgg
ggucggcggcgaugucggcuacccacccgacccgucuugaaacacggacc
aaggagucuaacacgugcgcgagucgggggcuacgaaagccgccguggcg
caaugaaggugaaggccgggccgaggugggaucccgaggccucuccaguc
cgccgagggcgcaccaccggcccgucucgcccgccgcgccggggaggugg
agcacgagcgcacguguuaggacccgaaagauggugaacuaugccugggc
agggcgaagccagaggaaacucugguggagguccguagcgguccugacgu
gcgaaucggucguccgaccuggguauaggggcgaaagacuaaucgaacca
ucuaguagcugguucccuccaaaguuucccucaggauagcuggcgcucuc
gcaguuuuauccgguaaagcgaaugauuagagguaccuauucucaaacuu
uaaauggguaagaagcccggcucgcugguguggagccgggcguggaaugc
gagugccuagugggccacuuuugguaagcagaacuggcgcugcgggauga
accgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccaga
aaagguguugguugauauagacagcaggaugguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccugccgaaucaacuagcccugaa
aauggauggcgcuggagcgucgggcccauacccggccgucgcuggcaguc
ggcagagcgagaaagagagugggcggacgcuacgccgcgacgaguaggag
ggccgcugcggugagccuugaagccuagggcgcgggcccggguggagccg
ccgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuu
gaaggccgaaguggagaaggguuccaugugaacagcaguugaacaugggu
cagucgguccugagagaugggcgagcgccguuccgaagggacgcucagcc
gaucgaaagggagucggguucagauccccgaauccggagcggagaugggc
guccagugcgguaacgcgaccgaucccggagaagccggcgggagccccgg
ggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguucg
ccccgagagaggggcccgugccuuggaaagcgucgcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggccgacuuagaacuggugcggaccagggga
auccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggugu
ugacgcgaugugauuucugcccagugcucugagucaaagugaagaaauuc
aaugaagcgcggguaaacggcgggaguaaugacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggaugaacgagauucc
cacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuu
ggcggaaucagcggggaaagaagacccuguugagcuugacucuagucugg
cacggugaauucacugacccggugaggcgggggggccucgcuucuggcgc
caagcgcccgcgggcgcgacccgcuccggggacagugccagguggggagu
uugacuggggcgguacaccugucaaacgguaacgcagguguccuaaggcg
agcucagggaggacagaaaccucccguggagcagaagggcaaaagcucgc
uugaucuugauuuucaguacgaauacagaccgugaaagcggggccucacg
auccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuacca
cagggauaacuggcuuguggcggccaagcguucauagcgacgucgcuuuu
ugauccuucgaugucggcucuuccuaucauugugaagcagaauucaccaa
gcguuggauuguucacccacuaauagggaacgugagcuggguuuagaccg
ucgugagacagguuaguuuuacccuacugaugauguguuguugccauggu
aauccugcucaguacgagaggaaccgcagguucagacauuugguguaugu
gcuuggcugaggagccaauggggcgaagcuaccaucugugggauuaugac
ugaacgccucuaagucagaaucccgcccaggcggaacgauagcgccggag
ccucgguuggccucggauagccggccggugcggagagcccuucgucccgg
gaaacgggccggaaaggggccgcgcccgucacgcaccgcacguucguggg
gaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuu
cguacguagcagagcagcugcgaucuauugaaagucagcccucgacacaa
ggguuugu
.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..[[[..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<.<<<<<<..<.<<<<<<<<....<<<<.....
.>>>>...((......<<<.....))>>>...>.>>>>>>>...>.>>>>
>>...>>>>>>>>>.......<<<<<<<........>>>>>>>.....((
(((..<<<<<<)))))..]]].............................
.....<<....>>...............<<<<....>>>>..........
........................<<<<<<<<..<<<.<<...<<<<<<<
<.<<<....<<<<<<<<<<<<<<<<<<.<<<<<<<<<<<<.<<..>>>>>
>>>>>>>>>>>>>...>>>>>>>>>>>>>>......>>>.>>>>>>>>..
.<<<<<<<<<<<<<<<<<<.<<<<...<<..<<<.<<..<<<......<<
<<<..>>>>>.......>>>..>>..>>>.........>>>>>>...>>>
>>>>>>>.....<<.......>>......<<<<<<.<<<<<<..>>>>>>
...<.<<..<<<.<<<<<<<<<<<<<<.<<<<<<<.<<<<..>>>>.>>>
>>>..>..>>>>>>>>>>>.>>>...>>>>>.>.......>>>>>>....
.>>>.>>>>>...>>>>>...>>>>>>>>..<<<<........>>>><<<
<<<....<<<<<<<<<<<<<..<<<...<<<<.....>>>>.....>>>.
..<<....>>...<<<<.>>>>..<<<<<...<<<..<<.....(((.[[
..>>..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>
.>>....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<.
.<<<....<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<...
.....>>>>.>>>....>>>>>>>>>...<<.......>>......>>>>
>>...>..>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<..
<<<.<<<<<<<<<...<<<....<<<..<.<<<..>>>.>..>>>..>.>
>...>>>>>>>...<<<<<<<<<.<......>>>>>>>>>>....>>>>>
>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>....<<<.....
.>>>...<<<<<<<...<<<(((.......<<<<<......<........
..<<<.<<<<<<<<<<.......<<<<<.<<....<<.........>>..
..>>.........<<......>>...>>>>>...>>>>>>>>>>>>>...
.......))).>....>>>>>..>>>...>>>>>>><<<<<<.<<<....
................]].)))...........>>>>>>>>>....>>>>
>>...<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>
>>>>>>........>>>>>><<.....<<.....<<<<<<.......>>>
>>>.<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<....<<<....>>>..........<<...>>....
..>>....>>>..<<<<<........>>>>>))<<<<.<<<<<..<<<<.
.>>>>..<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<
<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<.....<<<....
.>>>.....>>>>>>>>..>>>>>.....<<<<<..>>>>>>>>>...>>
>>>>>>>>>>.........>>>>>>>..>..........>>.>>>.>>>>
.>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>...
.<<<<.....<<<<<<<.<<.........<.....<<<<<..........
.....>>>>><<.<<<<<<......>>>>>>.>>............<<<<
<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>>..
....>>>>>>>...<<..<<<..<<<<<<...<<.....<<<<....>>>
>.....>>..>>>>..>>>>><<<<<<....>>>>>>........<....
.......<<<<<.......>>>>>.....>.....>>....>>.>>>>>>
>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>
>>....[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<
<<<.<<<<..>>>>...<<<<<.....<<<<..<<..>>...........
...<<<<<<..>>>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>
...<<<.....>>>..<<<<<<...........>>>>>>..<<...<<<<
<<<...<<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>
>...<<<..<<<<.......>>>>..>>>.<<<....>>>.>>)))]...
...((((((..(((..>>>>>>.)))))))))..........]]]]..}}
]]]].......<<.<.<.<<<<<<...<<.......>>...>>>>>>...
>>.>.>.......<<<<<.<<<<<<..<.<.<<<<<......>>>>>...
>.>.<<<.........>>>.....>>>>>..>...>>>.>>....<<<<<
<<....>>>.>>>>....}}..}}}.]]]]].....<<<<<<.<..<<<.
.<.<<<<<.................>>>>>.><<<<....<<<<....<<
.<<<<<<.}}}..>>>>..>>.>>...>>>>...>>>><<<<....<<<<
<...........>>>>>....>>>>.>>>...>.>>>>>>.<<<<<<<..
<<<<....<<<........<<<<..>>>>.......>>>...<<<..<<<
<......<<<.......>>>....>>>>..>>>..............>>>
>..>.>>>>>>.<<<<<.<.............>....<<.<<<<<<<.<<
.....<<<<....<<<..>>>...>>>>....>>....>>>>.>>>.>>.
.>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7oyd A molecular network of conserved factors keeps ribosomes dormant in the egg.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
K2 A3 S4 G5 Y63 Q66 F68 K70 P72 S86 R87 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 R139 H146 D147 P155 H156 R157 V158 R160 R161 H163 R166 T169 K170 R171 P172 N173 T174 F175 F176
Binding residue
(residue number reindexed from 1)
K2 A3 S4 G5 Y63 Q66 F68 K70 P72 S86 R87 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 R139 H146 D147 P155 H156 R157 V158 R160 R161 H163 R166 T169 K170 R171 P172 N173 T174 F175 F176
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Tue Dec 3 00:42:44 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 = '7oyd', asym_id = 'S', bs = 'BS01', title = 'A molecular network of conserved factors keeps ribosomes dormant in the egg.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7oyd', asym_id='S', bs='BS01', title='A molecular network of conserved factors keeps ribosomes dormant in the egg.')
   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 = '7oyd', asym_id = 'S'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='7oyd', asym_id='S')
    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>