Structure of PDB 5xxb Chain f Binding Site BS01

Receptor Information
>5xxb Chain f (length=107) Species: 5811 (Toxoplasma gondii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APRLVYRRHNHYATGSNRVRRVRTPGAKVVFHNVGKQPSRPKCGNCHRAL
PGIPAVAPHRLRLLKKRERTVHRAYGGSRCHACVRERIVRAFLVEEQKCV
KQVLQVK
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)		A2 R4 L5 V6 Y7 R8 R9 H10 N11 H12 Y13 T15 S17 R19 R21 R22 V23 R24 T25 P26 G27 H33 K37 Q38 S40 R41 P42 K43 R49 P52 G53 P55 P59 H60 L62 R63 L64 K66 K67 R68 R70 T71 V72 H73 R74 Y76 G78 R88 R91 A92 V95 Q98
Binding residue
(residue number reindexed from 1)		A1 R3 L4 V5 Y6 R7 R8 H9 N10 H11 Y12 T14 S16 R18 R20 R21 V22 R23 T24 P25 G26 H32 K36 Q37 S39 R40 P41 K42 R48 P51 G52 P54 P58 H59 L61 R62 L63 K65 K66 R67 R69 T70 V71 H72 R73 Y75 G77 R87 R90 A91 V94 Q97
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Wed Apr 30 04:06:37 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 = 'f', 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='f', 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 = 'f'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='5xxb', asym_id='f')
    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>