Structure of PDB 5ndv Chain O7

Receptor sequence

>5ndvO7 (length=84) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]

GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGA
KAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASK

3D structure

PDB

5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.

Chain

Resolution

3.3 Å

3D
structure

Enzymatic activity

Enzyme Commision number

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)
BS01	rna	O7	G2 K3 G4 T5 P6 F8 G9 K10 R11 H12 N13 K14 S15 H16 R24 R25 S26 H28 Q30 S35 A42 K43 T44 R45 Y47 N48 W49 K52 R55 R56 T58 T59 S71 K75	G1 K2 G3 T4 P5 F7 G8 K9 R10 H11 N12 K13 S14 H15 R23 R24 S25 H27 Q29 S34 A41 K42 T43 R44 Y46 N47 W48 K51 R54 R55 T57 T58 S70 K74
BS02	rna	O7	T17 R21 C22 G23 V29 K32 A42 T59 G60 T61 G62 R63 M64 R65 Y66 L67 K68 R72 F74 K75 N76 Q79 T80 G81 S82 A83 S84 K85	T16 R20 C21 G22 V28 K31 A41 T58 G59 T60 G61 R62 M63 R64 Y65 L66 K67 R71 F73 K74 N75 Q78 T79 G80 S81 A82 S83 K84
BS03	ZN	O7	C19 C34 C37	C18 C33 C36
BS04	MG	O7	S46 Y47 G50	S45 Y46 G49

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0008270	zinc ion binding
GO:0019843	rRNA binding
GO:0046872	metal ion binding

	Biological Process
GO:0000448	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0002181	cytoplasmic translation
GO:0006412	translation

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005840	ribosome
GO:0022625	cytosolic large ribosomal subunit
GO:0030687	preribosome, large subunit precursor
GO:0044391	ribosomal subunit
GO:1990904	ribonucleoprotein complex

External links

PDB	RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
PDBsum	5ndv
PubMed	29208708
UniProt	P49166\|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)