Structure of PDB 5xy3 Chain D Binding Site BS02

Receptor Information
>5xy3 Chain D (length=272) Species: 5722 (Trichomonas vaginalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKLVKNAGYFSRFQTKFRRRREAKTDYVQRTQLIQQDKTKYGAAKYRLV
ARITNTKVIAQIVVAELTGDKTVCQALSTELPKYGIKLGLSNYPAAYATG
LLVARRFLTQMKLADVFKTEITDEENRRPFKVILDVGLARTTTGAKVFAV
MKGAVDGGLFIPHNVQYYILGGAVADYMRKLKKESEEKYNKQFSRYVKAG
ITADNLEKIYKDAHAAIRKNPAATVIADKKKHAEEMKQKHAPKKPQTKKL
SFEEKRKILNEHLVAAGLPPRK
Ligand information
>5xy3 Chain 3 (length=117) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gaagcggccacacccggcuggcaacauccagcuccacuccgaaccuggaa
auuaagcagucgcgggccacaucaguacugggcugggcgacuucccggga
acgugcggugcuugcuu
<<...<<.....<<<<<<<<.....<<<<<<.............>>>>..
>>....>>>>>>.>><<<.<<<.....<<<<<..<<....>>.>>>>>..
..>>>.>>>.>>...>>
Receptor-Ligand Complex Structure
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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)
K7 F12 S13 F15 T17 F19 R20 R21 R23 T27 Y29 R32 R53 T55 N56 T57 K58 I60 Q62 T69 D71 T73 Q76 N93 Y94 R146 T149 G150 A151 K152 Y204 Y213 Q228 F229 S230 R231 Y232 M272 K273 H276 Q282 T283 K285 F288 R292 K308
Binding residue
(residue number reindexed from 1)
K6 F11 S12 F14 T16 F18 R19 R20 R22 T26 Y28 R31 R52 T54 N55 T56 K57 I59 Q61 T68 D70 T72 Q75 N92 Y93 R140 T143 G144 A145 K146 Y168 Y177 Q192 F193 S194 R195 Y196 M236 K237 H240 Q246 T247 K249 F252 R256 K272
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Cellular Component
External links
PDB RCSB:5xy3, PDBe:5xy3, PDBj:5xy3
PDBsum5xy3
PubMed28809395
UniProtA2DNM5

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