Structure of PDB 5xy3 Chain X Binding Site BS01

Receptor Information
>5xy3 Chain X (length=101) Species: 5722 (Trichomonas vaginalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRRPAFEHKAVKPVSLKHNDYKIIRGPVTSDKSTVKIENENTMTFWVDIK
ATKTEIAAAFNRLYKVKPVKVCTVITSKFVKKAYIRLPANVEAMNIATEI
G
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)		P38 R39 R40 A42 S67 K69 K73 E77 T89 K90 K107 C109 V111 I112 S114 K118 Y121 R123
Binding residue
(residue number reindexed from 1)		P1 R2 R3 A5 S30 K32 K36 E40 T52 K53 K70 C72 V74 I75 S77 K81 Y84 R86
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
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
UniProtA2DUV8

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