Structure of PDB 5xxb Chain C Binding Site BS01

Receptor Information
>5xxb Chain C (length=394) Species: 5811 (Toxoplasma gondii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATARPLVSVYKPEDGTASGTSLMPSVFLSPRPDLVRFVHTNMAKNRRQPY
GVAPNAGYQTSAESWGTGRAVSRIPRVPGGTHRAGQAGNMCRGGGMFAPN
KTWRRWHRKVNVTQKRHAVASAVAATGLPALVMARHRIDEVPELPLVVSE
KLEKVSKTREAVKILETLGCTAELERVRASAKKLRAGKGKMRGRRTHMRR
GPLVVYAEDNGVTRAFRNIPGVELCKVDSLNLLQLAPGGALGRFCLYTAS
AFKRLQLLFGRHTTGTAQLKKGYHLPRALMSNADLSRIVNSEEIQRVVRP
ARVARGQKKNLLKNHAVLCRVNPAARNLKILARLAQTEGTKQRALVLRKK
QANREEHKKHRQSARRFAAEIRQAFSDKMAAELEAAARRKAEEA
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 R5 P6 L23 R33 D35 L36 R38 F39 T42 K46 N47 R48 R49 Q50 Y52 V54 A55 A58 Y60 Q61 S63 T69 G70 A72 V73 S74 R75 P77 G82 T84 H85 R86 Q89 A90 N94 M95 C96 R97 G98 M101 F102 A103 R109 R110 K114 N116 T118 Q119 K120 R121 H122 R140 K163 T164 R165 R182 K188 K189 L190 R191 A192 G193 K194 K196 M197 R198 R200 H203 R205 R206 R220 R223 N224 D234 S235 N237 P243 G244 Q262 R267 Q275 L276 K277 K278 R294 N297 S298 E299 Q302 R306 A308 R309 A311 R316 Q318 N321 N325 H326 R337 N338 K340 Q347 R354 K361 R365 E367 H368 H371 R372 Q373 F378 A379 R383 K401
Binding residue
(residue number reindexed from 1)
A1 R4 P5 L22 R31 D33 L34 R36 F37 T40 K44 N45 R46 R47 Q48 Y50 V52 A53 A56 Y58 Q59 S61 T67 G68 A70 V71 S72 R73 P75 G80 T81 H82 R83 Q86 A87 N89 M90 C91 R92 G93 M96 F97 A98 R104 R105 K109 N111 T113 Q114 K115 R116 H117 R135 K157 T158 R159 R176 K182 K183 L184 R185 A186 G187 K188 K190 M191 R192 R194 H197 R199 R200 R214 R217 N218 D228 S229 N231 P237 G238 Q256 R261 Q268 L269 K270 K271 R287 N290 S291 E292 Q295 R299 A301 R302 A304 R305 Q307 N310 N314 H315 R326 N327 K329 Q336 R343 K350 R354 E356 H357 H360 R361 Q362 F367 A368 R372 K390
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Wed Apr 30 04:06:59 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 = 'C', 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='C', 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 = 'C'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='5xxb', asym_id='C')
    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>