Structure of PDB 5ndv Chain m0

Receptor sequence

>5ndvm0 (length=219) Species: 559292 (Saccharomyces cerevisiae S288C)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
MLSCAGADRLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEG
LRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLS
KKGSLENNIREFPEYFAAQ

3D structure

• PDB: 5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: m0
• Resolution: 3.3 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	m0	R3 R4 A6 R7 C8 K13 N14 K15 Y22 Y34 D35 K39 A64 A67 K74 R90 H92 F94 R98 D109 R110 L111 Q112 Q113 G114 M115 R116 A118 W119 Y157 K158 P160 D193 G194 A195 F196 K198	R2 R3 A5 R6 C7 K12 N13 K14 Y21 Y33 D34 K38 A63 A66 K73 R89 H91 F93 R97 D108 R109 L110 Q111 Q112 G113 M114 R115 A117 W118 Y156 K157 P159 D192 G193 A194 F195 K197
BS02	rna	m0	Y11 E56 L57 K202 K203 G204 S205 L206	Y10 E55 L56 K201 K202 G203 S204 L205
BS03	PAR	m0	L111 Q112	L110 Q111
BS04	MG	m0	R156 Q163	R155 Q162

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006415 translational termination

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
• PDBsum: 5ndv
• PubMed: 29208708
• UniProt: P41805|RL10_YEAST Large ribosomal subunit protein uL16 (Gene Name=RPL10)