Structure of PDB 5ndw Chain S5

Receptor sequence

>5ndwS5 (length=206) Species: 559292 (Saccharomyces cerevisiae S288C)

FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIF
VAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLD
IINVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVN
QAIALLTIGAREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELER
VAKSNR

3D structure

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: S5
• 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	S5	H72 A78 R81 K84 R92 N95 L97 M98 M99 N100 G101 R102 N103 N104 G105 K106 K107 L108 K109 R112 R166 N169 R180 F184 R185 N186 I187 T189 I190	H53 A59 R62 K65 R73 N76 L78 M79 M80 N81 G82 R83 N84 N85 G86 K87 K88 L89 K90 R93 R147 N150 R161 F165 R166 N167 I168 T170 I171
BS02	MG	S5	I187 K188 T189	I168 K169 T170
BS03	MG	S5	L25 A26	L6 A7

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000054 ribosomal subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity
• GO:0030490 maturation of SSU-rRNA

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P26783|RS5_YEAST Small ribosomal subunit protein uS7 (Gene Name=RPS5)