Structure of PDB 5ndg Chain m7

Receptor sequence

>5ndgm7 (length=175) Species: 4932 (Saccharomyces cerevisiae)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVT
EKEEAVVRLTSRQRGRIAAQKRIAA

3D structure

• PDB: 5ndg Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: m7
• 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	m7	A2 R3 Y4 A17 R18 Y21 R23 S25 F26 K27 N28 R30 Q34 Q50 Q55 R56 R62 F63 N64 S65 S66 I67 G68 R69 A71 Q72 K74 E75 T79 K80 R82 W83 P84 A85 K86 N97 N101 Q118 V119 N120 Q121 R127 T129 Y130 R131 A132 H133 G134 R135 N137 K138 Y139 E140 S141 T169 S170 R171 Q172 R173 G174 R175 A178 I182	A1 R2 Y3 A16 R17 Y20 R22 S24 F25 K26 N27 R29 Q33 Q49 Q54 R55 R61 F62 N63 S64 S65 I66 G67 R68 A70 Q71 K73 E74 T78 K79 R81 W82 P83 A84 K85 N96 N100 Q117 V118 N119 Q120 R126 T128 Y129 R130 A131 H132 G133 R134 N136 K137 Y138 E139 S140 T160 S161 R162 Q163 R164 G165 R166 A169 I173
BS02	rna	m7	R3 Y4 G5 A6 R61 R62 Q118 N120 Q121 P123 H145	R2 Y3 G4 A5 R60 R61 Q117 N119 Q120 P122 H144
BS03	MG	m7	S66 I67 G68	S65 I66 G67

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)