Structure of PDB 5xxb Chain n Binding Site BS01

Receptor Information
>5xxb Chain n (length=97) Species: 5811 (Toxoplasma gondii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNVPKLRNTFCKGPKCRKHQPHKVSQYKKGKDSLVVQGKRRYDRKQKGFG
GQTKPIFRKKAKTTKKIVLKLECTKCKTKRLLPIKRCKSFELGAEKK
Ligand information
>5xxb Chain 1 (length=3077) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaccugaaaucaggcgagguuacccgcugaacuuaagcauauuauuaag
cggaggagaagaaaauaacuaugauucccuuaguaacggcgagugaaccg
ggaucagcucaaaguggaaaucaacugcucuguugacuuguagccucgag
aggcguuaccaguggaagcgcaggguuaaguuucuugggaaagaacauca
uagagggugagaaucccguccuuccccugcguuuuuuguuccacguacgg
uacgcuuuuauagagucgcguucaucgggauuugagcgcaaaaugugugg
uagguuucacauaaagcuaaguacuggcgcgagaccgauagcaaacaagu
accgugagggaaagaugaaaaguucuuuggaaagagaguuaaaagugccu
gaaauugcugaaaaggaagcgauugggaccuugauuccaagaagugccgc
cgguuugccaucuaucccuuugccuucucucucucaccagguuuaggcuu
ugucuugauguauuuccgguucaucuuuuuggagaggucagcaucagcua
cucggaauugauuucguucaaagaagguagguuccuuguggaccguuaua
ucuuuguucuuuccuuuuccuuguggcugaggaguguuccuguuuccgag
cucgguuucugugaugcuggcuaucgguuccaaccgacgucuugaaacac
ggaccaaggagucuaacauaugugcgaguacggguuuuacuccuguaugc
gcaaugaaagugaaguagggagauuuugcuuugccauucuucgcaccuac
gaccgaccacgaucucugagagagguuugaguuggagcauaucuguuagg
acccgaaagauggugaacuaugccugaguagaaugaagucagggccugau
ggagguucguagcgauacugacgugcaaaucguucgucaaacuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuucuuccgaaguu
ucucucaggauagcuggaguuuuguuaguuuuaucagguaaagcgaauga
uuagaggcccucgaccuauucucaaacuuuaaauggguaagauccagugg
uuacuucauugaacugcugggauuaauaugacuccaagugggccauuuuu
gguaagcagaacuggcgaugagggaugcuccuaacgcuugguuaaggugc
caaaaugcucgcucaucagauaccauaaaagguguugguucauaugaacc
agcccugaaaauggauggcgcugaagcgggcuaccgauaccaggccauug
cuacuaauuaucacucgaccuuuuguagcaaugaguaggaagacgugggg
auugugacgaagcguucggcguaagccugcguggaacagucucuagugca
gaucuuggugguaguagcaaauauucaaaugagaacuuugaagacugaag
uggagaaggguuccaugugaacagcaauuggacauggguuagccgguccu
aagcgacagcuuaacugcguauacaguaccucguuucgcgaaagggaauc
ggguuaauauucccgagccaggacguggauacuguacgguaacguaagug
aacuccucgacgcaggcaggugcuccgggaagcguugucuuugcuuuuua
acagccacccuggaaucaguuuagcuggagauaggguuagcuggcuggua
gagcaccuuggaagguguccggugcgcuccugacugcccuugaaaagagg
agggaaaguuguuauuuacaccccuggccguaccaauaaccgcaucaggu
cuccaagguuaguagccucuggucgauagaauaagguagauaagggaagu
cggcaaaauagauccguaacuucgggaaaaggauuggcucugagggcugg
aacagcuaacucagaacuggagcggacaaggggaauccgacuguuuaauu
aaaacaaagcauugcgauggccauaacugguguugacgcaaugugauuuc
ugcccagugcucugucaaugugaugaaauuaaucaagcgcggguaaacgg
cgggaguaaugacucucuuaagguagccaaaugccucgucaucuaauuag
ugacgcgcaugaauggauuaacgagauucccacugucccuaucuacuauc
uagcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaag
aagacccuguugagcuugacucuaguccgacuuugugaaauuuacuuauu
ccguuaaguugagacucaugcucugcauguguuuugguuuuaagguggcc
cgcugaucuacgcggaagacacagucagguugggaguuuggcuggggcgg
cacaucugugaaacaauagcgcagguguccuaaggcaagcucaaugagaa
cagaaaucucauguugaccaaaaggggaaaagcuugcuugauuuugauuu
ucaguacgaauacaaacugugaaagcauggccuaucgauccuuuaggucu
gagaaacuuucagcuagaggugucagaaaaguuaccacagggauaacugg
cuuguggcagccaagcguucauagcgacguugcuuuuugauccuucgaug
ucggcucuuccuaucauugagacgcagaagucucaaagugucggauuguu
cacccgccaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugacuugauacugcgacaguaauccaacuuagu
acgagaggaacaguugggucggauacuugguaaaugcggcuagcugaaaa
gcuagugccgcgacgcuaccauccguuggauuaugacugaacgccucuaa
gucagaauccaugcuggauaugcaguguuauucaccgccuccuuuguuuc
augcaaugauacaggccucuggccugcuucucaucaaagcccugggcgag
aaucucaauuucuaacauuggaggugauacauccauugcagacgacuuug
uugcaaccggguauuguaaguaugagaguaggcuugucuacgaucuacua
agauuuuuccugcguuguucgaugugg
.......................<<<<<<.....<<....>>......>>
>>>.>.........<<....>>...<<<<......<<.....>>.....>
>>>...<<<...........<<<<<......>>>>>............<<
<<<<<.<<<<.<<<<<.<<<<<<<<......<<<<......>>>>.((..
....<<<.....))>>>.......>>>>>>>>.......>>>>>....>>
>>>>>>>>..>......<<<<<<<........>>>>>>>.....<<<<<.
.((((((>>>>>..>>>.................................
.<<....>>..............<<<<<....>>>>>.............
...................<<.<<<<<<<<.....<<<<<<<<<<...<<
<<<...................<<<...<<.<......>>>...>>>...
..............>>.>>>..>.>>>>>>>>>..<<<<<<<<<<<<<<<
<..<<<<........<..<<<<<<.....<<<<<.....>>>>>......
>>>>>>..>.......>>>>..>>>>>>>>.((((....<.<...<<<<.
.>>>>...>.>...>>>>>>>>...>>>>>>>>.>>..<<........>>
..<<<<<<...<<<<<<<.<<<<<<..<<<.<<<.......>>>...>>>
...<<....>>...<<<<<..<<....<<...>>......>>...>>>>>
<<<<<<<<.<..<<...>>..>.>>.>>>.>>>...>>>>>>.>>>>>>>
.<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<.>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<.<....<<.<<<<<<<.....<<<....<<<
....<<<.......>>>....>>>..>>.>.....>>>>>...<<<<<<<
<<.<......>>>>>>>>>>....>>>>..>>>>>>.>>..<<<<.<<<<
<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<((
(.....<<<<<<......<..........<<<.<<<<<<<<<..>>>>>>
>>>>>>..........))).>....>>>>>>.>>>...>>>>>>><<<<<
<<<<........))))........>>>>>>>>>....>>>>>><.<<<<<
<<<<<......<<<<..<<<....>>>.>>>>...>>>>>>>>>>..>..
...>>>>>><<<....<<.....<<<<<<.......>>>>>><<<<....
.<<<<<.<<...<<<<<....<<.....>>..>>>>>....((<<<<<<.
..<<<<..<<......>>.................>>>>....>>...<<
<<<........>>>>>))<<<<..<<<<<<<....<<<....>>>.....
.{<<<<<<...<<<<.<<<<.<<.<<<<<<<<<<...[[..>>>>>>...
.<<<<<<<<<<<....<<<<...>>>>....>>>>>>.....>>>>>...
..<<<<<<<..>>>>>>>>>>>...>>.>>>>.>>>>.........>>>>
>>..........>>>>..>>>.>>>>>>>>..>>.....<<......>>>
>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<.....
....<.....<<<<<.....<..>......>>>>><<.<<<<<<<<<<<.
..>>>>>..>>>>>>.>>............<<<<<<<<<..<<<......
...>>>..<<<<<<<....<<<<....>>>>......>>>>>>>...<<.
.<<<..<<<<<<.<<.......<......>......>>..>>>>..>>>>
><<<<<<....>>>>>>........<...........<<<<<.......>
>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>>.>>
>>>>...>>>....<<<<<........>>>>>....<<<<<..<<<.<<.
.....<<<<.<<<<<<..<<<<<.<<<.<<<<..<<<<<.>>>>>...<<
<<<.....<.<<..<.<<.........>>.>........}...<<<<<.>
>>>>..>>.>..>>>>>.....>>>>.>>>..>>>>>...<<<.....>>
>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.
......>>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<<<
.......>>>>.>>>>.<<<....>>>.>>)))......<<<<<<<..<<
<<.))))))>>>>>>>>>>>.........>>>>..>>>>>>.......<<
.<.<.<<<<<<...<<.......>>...>>>>>>...>>.>.>.......
<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<......
...>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>
>....>>..>>>.>>>>>.....<<<<<<<<..<<<<.<<<<<<<<....
...........>>>>>>>><<<<<...<<<<....<<<<<<<<<.]]...
>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...........>
>>>>...>>>>.>>>>.....>>>>>>>>......<<<<<<<..<<<<..
.............<<<<...>>>>................<<..>>....
.............>>>>..>>>>>>>..<<<<<<<.............>>
..<<<<<<<<<.<<<....<<<.<<..<<<<<<..>>>>>>..>>>>>..
.>>>....>>>>.>>>>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5xxb Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
Resolution3.17 Å
Binding residue
(original residue number in PDB)		V2 N3 P5 R8 N9 F11 K13 K19 H20 Y28 K30 D33 V36 V37 Q38 G39 R41 R42 R45 K46 K48 G49 F50 G52 Q53 T54 K55 P56 I57 F58 R59 K61 A62 K63 T65 K67 K80 R81 K86 R87 C88 K89 K98
Binding residue
(residue number reindexed from 1)		V1 N2 P4 R7 N8 F10 K12 K18 H19 Y27 K29 D32 V35 V36 Q37 G38 R40 R41 R44 K45 K47 G48 F49 G51 Q52 T53 K54 P55 I56 F57 R58 K60 A61 K62 T64 K66 K79 R80 K85 R86 C87 K88 K97
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Wed Apr 30 04:17:18 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 = '5xxb', asym_id = 'n', bs = 'BS01', title = 'Cryo-EM structures of the 80S ribosomes from hum...sites Trichomonas vaginalis and Toxoplasma gondii'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5xxb', asym_id='n', bs='BS01', title='Cryo-EM structures of the 80S ribosomes from hum...sites Trichomonas vaginalis and Toxoplasma gondii')
   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 = '5xxb', asym_id = 'n'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='5xxb', asym_id='n')
    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>