Structure of PDB 5ndv Chain l7

Receptor sequence

>5ndvl7 (length=223) Species: 559292 (Saccharomyces cerevisiae S288C)

TAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKA
AGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTK
ATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEA
NLGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFK
HFIQGGSFGNREEFINKLVKSMN

3D structure

• PDB: 5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: l7
• 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	l7	R41 R60 R67 K70 K90 G91 I92 N93 K94 P97 K98 K101 L105 R107 R110 I111 N112 K121 A122 E125 L126 Y141 S142 R145 K150 R151 K155 K158 Q159 R160 K196 N200 K206 L207 S208 N209 P210 S211 G212 G213 W214 P217 R218 K219 K241	R20 R39 R46 K49 K69 G70 I71 N72 K73 P76 K77 K80 L84 R86 R89 I90 N91 K100 A101 E104 L105 Y120 S121 R124 K129 R130 K134 K137 Q138 R139 K175 N179 K185 L186 S187 N188 P189 S190 G191 G192 W193 P196 R197 K198 K220
BS02	rna	l7	K128 E131 R218 K221 H222 Q225	K107 E110 R197 K200 H201 Q204
BS03	MG	l7	T120 K121	T99 K100

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

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: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)