Structure of PDB 5ndg Chain m6

Receptor sequence

>5ndgm6 (length=197) Species: 4932 (Saccharomyces cerevisiae)

VEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKL
KYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERL
KVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDV
VAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY

3D structure

• PDB: 5ndg Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: m6
• 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	m6	P5 V6 K12 L15 V16 G17 R18 S21 K25 K32 S44 F48 R49 H55 R59 K60 A61 T62 A63 F64 K66 R68 P70 F71 H72 F73 R74 K82 A83 R85 G86 M87 V88 S89 H90 K91 T92 A93 R94 K96 E100 R101 G107 I108 P109 P110 K114 K116 R117 Q122 R128 L129 K130 R133 K134 S144 V145 G146 K148 Y149 L156 K159 R160 K161 S164 Y167 Y168 K171 R172 K176	P3 V4 K10 L13 V14 G15 R16 S19 K23 K30 S42 F46 R47 H53 R57 K58 A59 T60 A61 F62 K64 R66 P68 F69 H70 F71 R72 K80 A81 R83 G84 M85 V86 S87 H88 K89 T90 A91 R92 K94 E98 R99 G105 I106 P107 P108 K112 K114 R115 Q120 R126 L127 K128 R131 K132 S142 V143 G144 K146 Y147 L154 K157 R158 K159 S162 Y165 Y166 K169 R170 K174

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P26784|RL16A_YEAST Large ribosomal subunit protein uL13A (Gene Name=RPL16A)