Structure of PDB 5xy3 Chain i Binding Site BS01

Receptor Information
>5xy3 Chain i (length=73) Species: 5722 (Trichomonas vaginalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLHSSGKRVNFARKIVHELVGWQPYERHTMDLIKIERRRAARQFLKKRLG
THRRAMKKLNTLEEVVQEESLHH
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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)
H18 S19 S20 G21 R23 R28 Q38 Y40 R52 R54 K61 K62 R63 L64 G65 R69 K72
Binding residue
(residue number reindexed from 1)
H3 S4 S5 G6 R8 R13 Q23 Y25 R37 R39 K46 K47 R48 L49 G50 R54 K57
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit

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
UniProtA2EXW7

[Back to BioLiP]