Structure of PDB 5xy3 Chain I Binding Site BS01

Receptor Information
>5xy3 Chain I (length=195) Species: 5722 (Trichomonas vaginalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRRPARCYRYIGNKPYPKSRFCRGVPDPRIIRYETGTKTAHAKELPICCR
LILLEHECVSSEALEAARVSSNRYMMKTMGKDGYHIKINLHPFHVLRINK
MLLQTGMRHAFGKPEGLVARANYNSQIMTIRTTSAGLKHALEALRRASFK
FPGHSRVVISNKVGFTPYTFEQFKELQANGQIVDCGNHVKRVYRR
Ligand information
>5xy3 Chain 1 (length=2544) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
guagucugccauacgcaggaagacccgcugaacugaagcaucucauuaag
cggaggaaaagaaacuaacuaggauucccuuaguaaaggcgaucgaaaag
ggaacagcccaacgucuuaaucccgagggaaauguagucgguucaccuau
ugcacuggucuaagucagauggaaugcugcgcgauucagaguaaaagccu
cguaugaccaaccgcaagcuuacgauggaccggggagagucggauacuuu
gagaguagugucuuaagggggugguaugucccauccaaggcuaaauaacg
ugagagaccgauagauuacaaguagugugaacgaaagaugaaaagaacuc
uaaaacagagggugaaaaguuccugaacuugcuuaggguuaaggcuauuu
auaguacccgucuugaaacacggauuagggaguuuaucuguagugcgagu
cuuugcacguuaacuguaaaggcguagagaaagcaacuggcguuugcaug
gcuacugagcauuacugauaggacccgaaagguggugaacuuugccugca
cagguugaagucaggggaaacucugauggaggaccguacggguuauugau
gugcaaaucauuuuucugauguagguaaaggugcgaaagacucaucgaac
caccuaauagcugguuuccuccgaaguuucccucaggauagcuguaaugc
uaguuaaggggaguagaguauggguagagguacuuauuuccaaacuucga
accuccuuguuaggcauuuaccuaacuggaaaugcuuaaaugaauuagcg
uuacaagugggcucugaccgguaagcggucauggcgaaaugggaugaacc
auacgucugaauaaggugccgaaauguacuaucacugauaccauaaaggg
aguccauguauauacuagggccccgaaaaugaauggcgcauauaguacua
ccgaucucagacaucaguucuauugaacugagaguagggggauguggaca
uuuuugugaaggugcaaugugaguuggacuggaagaaugucuauuacaga
uccuaauugaaguagcgauuauccaggcuuguauccugggggcugaugag
gaguaggguuucuggacaacuuaaacagauccagaguuagucgauccuaa
ucucaauaaugggagaaagggaguacaguugauauucuguaacugacaac
aguucgcggcaacgcauacuauuuuucuccgccaaucuuauaccguuggu
agggaucucuuuccuacaugacaguacuaauacccagggaaacuggucau
caggcgaacugcggcguucugcuggcaaaacauagcuguuaugucaaugg
cuauuggauugguccaugaagcgaaaaauaguuuacuggucacucguacc
gauaaccgcaucaggucuucuagguaaguagccuauggccauugaggcau
gauaguucagggaauucggccaauuagagcuguaacuucgggauaaagcu
uggcucugaugaaaaucagaaccgauuguuacgcggagagcccaacuguu
uaauaaaaacguagugucgcgcugugguaguauagccagugaacgcgaca
ugaauccugcucagugcugugucuguuaauaugguucaagccaacgaagc
accgguaaauagcugggguaacuaugacucuuaucaaaguagcgaaauac
cucgucacuuaauuagugaccugcaugaacggagcuaugagguucucacu
gucccaaacugucucucagcgaaccaacuguagugggaacggucacuaga
uauccagcggggaaagaagacccuguagagcuucacuuuggucuagucuu
guauaguauuaugcuuaccuaucacaaggaauaggacuagauagaaaguu
uggcuggggcggcacaccuucgaaagagcagcgaagguguccuaaguuga
gcucagugaggacagaaaucucacguugaggauaaggccaaaagcucaau
uuacugugccuuuuuguacuaggaucaguuacgaaaguaaggccuaacga
ucccuaaauagccucaggugcgugaggauuggggugacagacaaguuacc
uccgggacaacuggcuuguggcugcuaagagaucaaaucaacgcagcuuu
uugauucuucgaugucggcucuuccuauccuagugauguacaaguugcua
agggucggauuguucacccguauuagggaucgugagcuggguuuagaccg
ucgugagccagguuuguuuuauccuacuggauauagcaucaugauaguag
auugauuuaguacgagaggaacuguugauuauggccucugguuagcgauu
aucggaaacgguaugucgcgcagcuacgccgucugggauaauggcugaaa
gccucuuaagccagaagcccaucuagaaagugaugcacuacgaauaaugg
uaacccaauguagaagacauugugugaacgaagguacuguaagcagugga
guggcaccacgaccuguugagguucagcuucgcuucuagguuuc
........................<<<<<.....<<....>>......>>
>>>...........<<....>>..<<<<<<......<.....>.....>>
>>>>..<<<......<<...<<<<..>>>>.....>>.<<<<<<<.<..<
<<<..<<<<<.....<<<........>>>.((......<<<.....))>>
>....>>>>>...>>>>......>.>>>>>>>.........<<<<<<<..
......>>>>>>>.....<<<<<..(((([[>>>>>..>>>.........
........................<<....>>...............<<<
<.....>>>>.................................<<<<<..
>>>>>..<<<<........>>>><<<<<<....<<<<<.<<<<<<<..<<
<...<<<.......>>>...>>>.............<<<<<....>>.>>
>.......>>>>>>>.>>>>>..<<.<..<<<<<<<.....<<<<<<<<<
..<<<....<<<<<<......>>>>>>.....>>>....<<<..<<.<<.
.......>>>>.>>>....>>>>>>>>>....<.......>.......>>
>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<.
...<<<<<<<<....<<<..<<<<...<<<..>>>...>>>>..>.>>..
..>>>>>>.<<<<<<<<<<.<<.....>>>>>>>>>>>>...>>....>>
>>>>>.>>..<<<.<<<<<<.....>>>>>>.>>>...<<<<......>>
>>..<<<<<<....<<<(((.....<<<<<<....<<..........<<<
.<<<<..<<<..>>>..>>>>>>>..........))).>>..>>>>>>.>
>>....>>>>>>.<<<<<<<....>>>>>>>.....>>>>>><.<<<<<<
<<<<......<<<.<<<<....>>>>.>>>...>>>>>>>>>>..>....
.>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<.....<
<<<..<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<<...
<<<<......>>>>....>>>..<<<<<........>>>>>))<<<<..<
<<<...<<....>>...<<<<<<<<<<...<<<<<<<<.<<<<<<<<<<<
<<<<...{{..>>>>>>....<<<<...<<<.<<<<<.....<<<<...>
>>>.....>>>.>>.>>>..>>>>.....<<<<<<<.>>>>>>>>>>>>>
.>>>.>>>>>>>>.........>>>>>>>>>>..>>>>>>>>.>>>..>>
.....<<......>>.>>>>.<<<<.....>>>>..>>>>..<<<<<...
<<<<<<<..<<...............<<<<<....<....>.....>>>>
><<.<<<<<<....>>>>>>.>>............<<<<<<<<<..<<<.
........>>>..<<<<<<<....<<<<......>>>>......>>>>>>
>...<<<.<<<..<<<<<..<..<<<<....<<<<....>>>>....>>>
>>.>>>..>>>>>.<<<<<.......>>>>>..........<........
...<<<<<<.....>>>>>>.....>....>>>....>>.>>>>>>>...
..>>..>>>>>>>>>>>>>>....>>....<<<<<........>>>>>..
<<<<<<<..<<<.<<......<<.<.<<<<<<..<<<<<.<<<<<<<<<.
<<<<<<..>>>>>>...<<<......>>>....>>>>>>>>>..>>>>>.
..<<<.....>>>..<<<<<<...........>>>>>>..<<...<<<<<
<<...<<<<<<.......>>>>>>.....<<.((.((>>....>>>>>>>
...<<<.<<<<.........>>>.>>>>.<<<....>>>.>>))))....
..<<<<<....<<<<.]].))))>>>>.>>>>>..........>>>>..>
>>.>>.......<<.<.<.<<<<<<...<<.......>>...>>>>>>..
.>>..>>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>.
.>>>.<<<.........>>>....>>>>>..>...>>>.>>....<<<<<
.<....>.>.>>>>....>>..>>>.>>>>>>>..<<<<<<...<<<..<
<<<<<<.................>>>>>>><<<<<....<<<..<<<<<<
<<<.}}...>>>>.>>>>>...>>>..>>>>>..<<<.<..<<<<<....
........>>>>>...>>>>..>>>.....>>>>>>..............
.<<<<<<<<<.......>>>>>...<<<<<<<...<<<....<<<<.<..
<<<<..>>>>..>>>>>...>>>.....>>>>.>>>..>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5xy3 Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
Resolution3.2 Å
Binding residue
(original residue number in PDB)		R3 R4 P5 A6 R7 C8 R10 K15 P16 F22 R24 Y34 E35 K39 T40 S61 E63 R74 K88 N90 H92 F94 R98 Q112 G114 M115 R116 H117 A118 F119 F157 K158 P160 G194 N195 H196
Binding residue
(residue number reindexed from 1)		R2 R3 P4 A5 R6 C7 R9 K14 P15 F21 R23 Y33 E34 K38 T39 S60 E62 R73 K87 N89 H91 F93 R97 Q104 G106 M107 R108 H109 A110 F111 F149 K150 P152 G186 N187 H188
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5xy3, PDBe:5xy3, PDBj:5xy3
PDBsum5xy3
PubMed28809395
UniProtA2FVZ6

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