Structure of PDB 5xy3 Chain A

Receptor sequence

>5xy3A (length=237) Species: 5722 (Trichomonas vaginalis)

GHIVRAQRRGNGSVFQAHTHHRVGPAKFRALDASVISGMVKEIIHDPGRG
APLAKLIYKGFDSALVIAPEGIHTGQFIKCGAQADLHIGNILPLAQIPEG
TEICNVEHRPGDGGRYGRCSGDSCRVIGHTENYTRIQLPSGRKALVSNIC
RATLGIVAGGGRPEKPLLKAGNVHYKYKAKRHTWPVVCGIKMNPVDHRHG
GGSHQHMGAPGTVARSARPGQKLGLIASRRTGRRRGT

3D structure

• PDB: 5xy3 Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
• Chain: A
• Resolution: 3.2 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	G2 H3 I4 Q8 R9 R10 G11 N12 S14 V15 F16 A18 H19 T20 H21 R23 G25 H50 P52 R54 F71 R125 Y126 G127 R128 C129 S130 G131 D132 L148 S150 R152 G171 R172 P173 K175 P176 L177 L178 K179 A180 G181 H184 Y185 K186 K190 R191 H192 W194 P195 V196 V197 C198 G199 I200 K201 M202 N203 D206 H207 R208 H209 G211 G212 S213 H214 Q215 G218 P220 T222 V223 A224 R225 S226 R228 P229 Q231 K232 L233 G234 I236 A237 S238 R239 R240 T241 G242 R243	G1 H2 I3 Q7 R8 R9 G10 N11 S13 V14 F15 A17 H18 T19 H20 R22 G24 H45 P47 R49 F61 R115 Y116 G117 R118 C119 S120 G121 D122 L138 S140 R142 G161 R162 P163 K165 P166 L167 L168 K169 A170 G171 H174 Y175 K176 K180 R181 H182 W184 P185 V186 V187 C188 G189 I190 K191 M192 N193 D196 H197 R198 H199 G201 G202 S203 H204 Q205 G208 P210 T212 V213 A214 R215 S216 R218 P219 Q221 K222 L223 G224 I226 A227 S228 R229 R230 T231 G232 R233

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5xy3, PDBe:5xy3, PDBj:5xy3
• PDBsum: 5xy3
• PubMed: 28809395
• UniProt: A2E6Z8