Structure of PDB 5ndv Chain L5

Receptor sequence

>5ndvL5 (length=293) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]

AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRL
VVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYAT
GLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQ
RTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFG
GHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADP
AFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALA

3D structure

PDB

5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.

Chain

Resolution

3.3 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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	L5	D6 K8 Y12 R15 F16 Q17 P19 R23 G26 T28 D29 Y31 R35 L36 K43 Y44 T46 K48 R140 P141 F142 K143 F145 L146 I148 R152 T153 P174 H175 S176 N178 R179	D5 K7 Y11 R14 F15 Q16 P18 R22 G25 T27 D28 Y30 R34 L35 K42 Y43 T45 K47 R139 P140 F141 K142 F144 L145 I147 R151 T152 P173 H174 S175 N177 R178
BS02	rna	L5	A2 S13 S14 F16 T18 F20 R21 R22 R24 K27 T28 Y30 R33 R50 R54 T56 N57 K58 I61 Q63 I65 I69 G71 D72 V74 Y79 H90 G91 N94 W95 Q151 R152 T154 T155 G156 R158 P181 F185 Y198 H203 V204 Y207 L222 K224 Y226 F253 P255 T256 K259 F260 K262 Y265 A266 E268 S269 K270 Y272 Q274 K276 L277 K279 R282 V286 K289	A1 S12 S13 F15 T17 F19 R20 R21 R23 K26 T27 Y29 R32 R49 R53 T55 N56 K57 I60 Q62 I64 I68 G70 D71 V73 Y78 H89 G90 N93 W94 Q150 R151 T153 T154 G155 R157 P180 F184 Y197 H202 V203 Y206 L221 K223 Y225 F252 P254 T255 K258 F259 K261 Y264 A265 E267 S268 K269 Y271 Q273 K275 L276 K278 R281 V285 K288

Gene Ontology

	Molecular Function
GO:0003735	structural constituent of ribosome
GO:0005515	protein binding
GO:0008097	5S rRNA binding
GO:0019843	rRNA binding

	Biological Process
GO:0000027	ribosomal large subunit assembly
GO:0002181	cytoplasmic translation
GO:0006412	translation

	Cellular Component
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005840	ribosome
GO:0022625	cytosolic large ribosomal subunit
GO:1990904	ribonucleoprotein complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
PDBsum	5ndv
PubMed	29208708
UniProt	P26321\|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)

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