Structure of PDB 5xxb Chain D Binding Site BS01

Receptor Information
>5xxb Chain D (length=261) Species: 5811 (Toxoplasma gondii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKALKNKAYFKRYQVKYRRRRQGKTDYAARRALVLQDRNKYNAHKHRLVV
RLTNKRIICQVVYSTIEGDRVLATAESTELPRYGVKIGLTNYAAAYCTGL
LLARRVLKQLGMSETFEGVETGEEYHIEENFGERRPFKVLLDVGIVRTTV
GNRVFGAMKGAADGGLHVPHGIKKFPGYSYDPEAHRARILGLHVADYMRQ
LKEEDPEKYSAQFSQYIKNKIEADDIEAMYKNAHAQIRKNPDAVRHVKLT
KAQRRERVQQK
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)
V4 K5 L7 K8 K10 R15 Y16 Q17 K19 R23 D29 A35 K43 Y44 K48 M115 R138 R139 F141 L144 R151 F159 H174 G175 K178
Binding residue
(residue number reindexed from 1)
V1 K2 L4 K5 K7 R12 Y13 Q14 K16 R20 D26 A32 K40 Y41 K45 M112 R134 R135 F137 L140 R147 F155 H170 G171 K174
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Nov 15 23:40:52 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 = '5xxb', asym_id = 'D', 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='D', 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 = '0003735,0005840,0006412,0008097', uniprot = '', pdbid = '5xxb', asym_id = 'D'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0008097', uniprot='', pdbid='5xxb', asym_id='D')
    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>