Structure of PDB 5xy3 Chain D

Receptor sequence

>5xy3D (length=272) Species: 5722 (Trichomonas vaginalis)

SAKLVKNAGYFSRFQTKFRRRREAKTDYVQRTQLIQQDKTKYGAAKYRLV
ARITNTKVIAQIVVAELTGDKTVCQALSTELPKYGIKLGLSNYPAAYATG
LLVARRFLTQMKLADVFKTEITDEENRRPFKVILDVGLARTTTGAKVFAV
MKGAVDGGLFIPHNVQYYILGGAVADYMRKLKKESEEKYNKQFSRYVKAG
ITADNLEKIYKDAHAAIRKNPAATVIADKKKHAEEMKQKHAPKKPQTKKL
SFEEKRKILNEHLVAAGLPPRK

3D structure

• PDB: 5xy3 Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
• Chain: D
• 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	D	A3 K4 L5 K7 Y11 F15 Q16 K18 R22 T27 D28 Q34 Q37 K42 Y43 K47 L114 R133 R134 P135 F136 I139 V142 L144 R146 T147 F154 P168 H169 N170	A2 K3 L4 K6 Y10 F14 Q15 K17 R21 T26 D27 Q33 Q36 K41 Y42 K46 L113 R127 R128 P129 F130 I133 V136 L138 R140 T141 F148 P162 H163 N164
BS02	rna	D	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	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

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

External links

• PDB: RCSB:5xy3, PDBe:5xy3, PDBj:5xy3
• PDBsum: 5xy3
• PubMed: 28809395
• UniProt: A2DNM5