Structure of PDB 5ndw Chain L7

Receptor sequence

>5ndwL7 (length=222) Species: 559292 (Saccharomyces cerevisiae S288C)

AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAA
GSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKA
TLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEAN
LGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKH
FIQGGSFGNREEFINKLVKSMN

3D structure

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: L7
• 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	L7	R30 R33 K34 N37 R41 R60 I63 R67 K70 K90 G91 I92 N93 K94 P97 K98 K101 L105 R107 R110 I111 N112 A122 E125 L126 S142 R145 K150 R151 K155 K158 Q159 R160 D165 K196 N200 K206 L207 S208 N209 P210 S211 G213 W214 P217 R218 K219 F220 K241	R8 R11 K12 N15 R19 R38 I41 R45 K48 K68 G69 I70 N71 K72 P75 K76 K79 L83 R85 R88 I89 N90 A100 E103 L104 S120 R123 K128 R129 K133 K136 Q137 R138 D143 K174 N178 K184 L185 S186 N187 P188 S189 G191 W192 P195 R196 K197 F198 K219
BS02	rna	L7	E131 R218 K221 H222 I224 Q225	E109 R196 K199 H200 I202 Q203

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:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)