Structure of PDB 8v87 Chain P

Receptor sequence

>8v87P (length=164) Species: 1247190 (Saccharomyces cerevisiae BY4741)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRKYESSPSHIELVVTEKEEVVRLTS
RQRGRIAAQKRIAA

3D structure

• PDB: 8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Chain: P
• Resolution: 2.66 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	P	R3 Y4 S16 R18 Y21 R23 S25 F26 K27 R30 Q34 Q55 R62 F63 S65 S66 R69 A71 Q72 K74 K80 R82 W83 P84 K86 Q96 N97 A100 N101 Q118 V119 N120 Q121 R127 Y139 E140 S141 R167 T169 S170 R171 Q172 R173 G174 R175 R181	R2 Y3 S15 R17 Y20 R22 S24 F25 K26 R29 Q33 Q54 R61 F62 S64 S65 R68 A70 Q71 K73 K79 R81 W82 P83 K85 Q95 N96 A99 N100 Q117 V118 N119 Q120 R126 Y128 E129 S130 R147 T149 S150 R151 Q152 R153 G154 R155 R161
BS02	rna	P	R3 Y4 G5 R61 R62 N120 Q121 P123 H145	R2 Y3 G4 R60 R61 N119 Q120 P122 H134

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:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)