Structure of PDB 5obm Chain c3

Receptor sequence

>5obmc3 (length=150) Species: 559292 (Saccharomyces cerevisiae S288C)

GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIG
VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKH
LERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN

3D structure

• PDB: 5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: c3
• Resolution: 3.4 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	c3	H123 K140	H122 K139
BS02	rna	c3	G2 R3 M4 H5 S6 G8 K9 G10 I11 S12 S13 S14 A15 P17 R20 P47 S48 G51 V52 R55 T61 R64 K70 M72 R73 K76 D87 Y90 L91 K94 S97 H101 R104 R106 K107 D108 D110 K112 F113 R114 I116 R121 R124 R127 Y128	G1 R2 M3 H4 S5 G7 K8 G9 I10 S11 S12 S13 A14 P16 R19 P46 S47 G50 V51 R54 T60 R63 K69 M71 R72 K75 D86 Y89 L90 K93 S96 H100 R103 R105 K106 D107 D109 K111 F112 R113 I115 R120 R123 R126 Y127
BS03	MG	c3	F26 K27 L28	F25 K26 L27

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5obm, PDBe:5obm, PDBj:5obm
• PDBsum: 5obm
• PubMed: 29208708
• UniProt: P05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)