Structure of PDB 8v87 Chain N

Receptor sequence

>8v87N (length=189) Species: 1247190 (Saccharomyces cerevisiae BY4741)

GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRL
GYKAKQGFVIYRVRVRRGNRKRPVNELKYQRSLRATAEERVGRRAANLRV
LNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLT
ATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWRYRK

3D structure

• PDB: 8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Chain: N
• 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	N	G2 Y4 E8 R12 K14 Q15 N34 V35 R41 R44 K47 R49 R50 K54 A55 Q57 R67 R68 G69 N70 N90 Q95 R96 R105 R108 N112 Q138 K140 R144 R147 W150 P154 H156 K157 H158 R162 L164 A166 K169 S171 R172 I174 K176 G177 H178 K179 F180 N181 N182 R187 R188 K189 W191 K192 R193 Q194 W200 R201 Y202 R203 K204	G1 Y3 E7 R11 K13 Q14 N33 V34 R40 R43 K46 R48 R49 K53 A54 Q56 R66 R67 G68 N69 N75 Q80 R81 R90 R93 N97 Q123 K125 R129 R132 W135 P139 H141 K142 H143 R147 L149 A151 K154 S156 R157 I159 K161 G162 H163 K164 F165 N166 N167 R172 R173 K174 W176 K177 R178 Q179 W185 R186 Y187 R188 K189
BS02	rna	N	R38 Q57 Y62 R109 N112 D136 H139	R37 Q56 Y61 R94 N97 D121 H124

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: P05748|RL15A_YEAST Large ribosomal subunit protein eL15A (Gene Name=RPL15A)