Structure of PDB 5t62 Chain c

Receptor sequence

>5t62c (length=183) Species: 559292 (Saccharomyces cerevisiae S288C)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVT
EKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

3D structure

• PDB: 5t62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
• Chain: c
• Resolution: 3.3 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	c	R3 R18 Y21 R23 S25 K27 R30 Q34 Q55 R62 F63 S65 S66 I67 G68 R69 A71 Q72 K80 R82 W83 K86 Q96 N101 H116 Q118 V119 Q121 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 K138 Y139 E140 S141 T169 S170 R171 Q172 G174 R175 A178 I182	R2 R17 Y20 R22 S24 K26 R29 Q33 Q54 R61 F62 S64 S65 I66 G67 R68 A70 Q71 K79 R81 W82 K85 Q95 N100 H115 Q117 V118 Q120 R126 T128 Y129 R130 A131 H132 G133 R134 I135 N136 K137 Y138 E139 S140 T168 S169 R170 Q171 G173 R174 A177 I181
BS02	rna	c	R3 Y4 G5 R61 R62 N120 Q121 P123	R2 Y3 G4 R60 R61 N119 Q120 P122

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:5t62, PDBe:5t62, PDBj:5t62
• PDBsum: 5t62
• PubMed: 28179369
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)