Structure of PDB 5ndg Chain m0

Receptor sequence

>5ndgm0 (length=209) Species: 4932 (Saccharomyces cerevisiae)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
QGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQ
QKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLENNIRE
FPEYFAAQA

3D structure

• PDB: 5ndg Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: m0
• Resolution: 3.7 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 P16 Y22 Y34 D35 K39 K40 S61 A64 A67 R90 H92 F94 R98 N100 Q113 M115 R116 G117 A118 W119 G120 Y157 K158 P160 D193 G194 A195 K198	R2 R3 A5 R6 C7 K12 N13 K14 P15 Y21 Y33 D34 K38 K39 S60 A63 A66 R89 H91 F93 R97 N99 Q101 M103 R104 G105 A106 W107 G108 Y145 K146 P148 D181 G182 A183 K186
BS02	rna	m0	Y11 E56 L57 I131 K202 K203 S205 L206 N209 F217	Y10 E55 L56 I119 K190 K191 S193 L194 N197 F205

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