Structure of PDB 5xyi Chain A Binding Site BS01

Receptor Information
>5xyi Chain A (length=204) Species: 5722 (Trichomonas vaginalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVIKMMLAAKVYLGSTNLSFGMKPYVFTCRKDGTHVINLAMTYEKIKLAA
RMIYAVEEPKDVLASTKSFTRAVHKFAEFLGANYVEQRFTPGLFTNYSIK
NFCEPRLMIVCDPNTDSQAVHEAAYANIPCIALCDTDAHLDYVDCVIPCN
TKNKNSMGLVMWLLTREVLRLRGALTEWSVLPDLFFYRDAADEAKIAEAL
EAEG
Ligand information
>5xyi Chain 2 (length=1490) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
acuugguugauccugccaaggaagcacacuuaggucauagauuaagccau
gcaaguguuaguaacugcgaauagcucauuaauacgcucagaaucuauuu
ggcggggauagcagcagcaacucuggugcuaauacaugcuguuucuccag
augugaauuauggaggaaaaguugaccucgaggcacgccauucgacugag
ugaccuaucagcuuguacuuagggucuuuaccuagguaggcuaucacggg
uaacgggcgguuaccgucggacugccggagaaggcgccugagagauagcg
acuauauccacggguagcagcaggcgcgaaacuuucccacucgagacuuu
cggaggagguaaugaccaguuccauugguuacguggauagggguacgguu
uuccaccguaccgacuagcagagggcagucuggugccagcagcugcggua
auuccagcucugcgaguuugcucccauauuguugcaguuaaaacgcccgu
agucugaauuggccagcaauggucguacguauacguucacugugaacaau
caggacgcuuagaguauggccacaugaaugacucagcgcaguaugaaguc
uuuguuaaaacaagcucaaugagagccaucggggguagaucuaucucaug
acgagugguggaauacuuugacucaugagagagaagcugaggcgaaggcg
ucuaccuagaggguuucugucgaucaagggcgagaguaggaguauccaac
aggauuagagacccugguaguuccuaccuuaaacgaugccgacaggaguu
ugucauuuguuaauggcagaaucuuuggagaaaucauaguucuugggcuc
ugggggaaauacgaccgcaaggcugaaacuugaaggaauugacggaaggg
cacaccagggguggagccuguggcuuaauuugaaucaacacggggaaacu
acccaggaccagauguuuaugacugacaggcuucgggucuuucaggauau
uguuuuugguggugcauggccguugguggugcguggguugaccuguccgu
ugauucagcuaacgagcgagauuaucgccaauuauuuacuuugccgaagu
ccuucgguuaaaguucuaauugggacucccugcguagcagguggaagagg
guagcaauaacagguccgugaugcccuuuagaugcucugggcugcacgcg
ugcuacaauguuaggacaauaggagcgagccugagagggugcgcuacucu
uauaaucccuaacguaguugggauugacguuuguaaucagcgucaugaac
caggaaucccuuguaaaugugugucaacaacgcacguugaauacgucccu
gcccuuuguacacaccgcccgucgcuccuaccgauuggaugacucgguga
aaucaccggauggaaagugauuaaaucacguuaucuagaggaaggagaag
ucguaacaagguaacgguaggugaaccugccguuggauca
..<<<<<.[.((((>>>>><<.<<<<.<<...<<<<<<<......<<<.<
<<..<<....<<.>>.>>......<<........<<<<<<...<<....<
<<<<..<...<<<.<<.......>>.>>>.....>......<<<<<<<<.
..<.....>.>>>>>>>>.......<<<..>>>..>>>>>...>>.>>>>
>>.<<<....<<<..<<<<<<<<.......>>>>>>>>>>>......>>>
...<<<.<<<<....>>>>.....>>>.>>.<<.<<<..........>>>
.>>.<<<<....>>>>...>>>>>>.........<<<....<<<<...>>
>>..>>>..>>.>>>>>...<<<<.<<....>>>>>>....<<<<<<<<.
....>>>>>>>>.....<<<<<((...<.<<<<.....<<..))>>....
...>>>>>>>>>>..>>.>>>>.>>.........<<<((.....<<<<..
.<<<.<<...<<<<......>>>>....<<..>>.<<<<<<<<<.....<
<<..<<.......>><<<....>>>...>>>.....>>>>>..>>>>...
...<<....>>....>>....<<<<<<.<...<<<<<<<<<..<<<<<<<
<...<<<......>>>......>>>>>>>>..>>.......<<....>>.
>>>>>>>...>>>>.>>>...>>>...>>>>..<.<<<<<<<...<...<
<<<.<.....>.>>>>...>>>>>>>>..>.......<<<.<<.<<<.<<
<<<<<<<....>>>>>>>>>.>>>...<<..))>>...>>.....>>>.>
>>.<<<......<.<<....>>.>....>>>..)))).]<<<<<.<<<<<
<<.<<..<<<<<..<<<.<<<<<<......<<........>>........
.<<<<<<...............<<<<.<<<.......>>>.>>>>.....
.......<<.<<<..<<.<<<<<<....<<.<<<<<<....>>>..<.<.
.....>.>...>>>.>>....<<<<<.<<<<<<<...<<<<<<<<<<<..
..>>>>>>.>>>>>..>>>>>>>.....<<<<<...>>>>>........>
>>>>....>>>.>>>.....>>>>>>>........>>>>>>..>>.>>>>
.>>>.....<<<<<<.....<<<.<<..<<<<....>>>>..>>....>>
>......>>>>>>...........<<<<<<<.......>>>>>>>.....
.....>>>>>.....<<<<<<<<.......>>>>>>>>......>>...>
>>>>>>>>>.>>....<..<<.<.<<<<<.<<....<<<<<<<..<<<..
<<<<<<..........>>>>>>..>>>..>>>>>>>...>>.>>>>>..>
.>>...>.....<<<<<<<<<....>>>>>>>>>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5xyi Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
Resolution3.35 Å
Binding residue
(original residue number in PDB)		F30 K41 R100 P103 G104 T107 N108 Q130 H133 E134 Y137 H151 D153
Binding residue
(residue number reindexed from 1)		F20 K31 R88 P91 G92 T95 N96 Q118 H121 E122 Y125 H139 D141
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small 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:5xyi, PDBe:5xyi, PDBj:5xyi
PDBsum5xyi
PubMed28809395
UniProtA2EFE7

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