Structure of PDB 8jdk Chain P

Receptor sequence

>8jdkP (length=170) Species: 9606 (Homo sapiens)

KENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTV
RSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGF
GIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRI
SKEEAMRWFQQKYDGIILPG

3D structure

• PDB: 8jdk Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Chain: P
• Resolution: 2.26 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	T56 R58 R64	T49 R51 R57
BS02	rna	P	K19 C21 N23 C25 S51 A53 R54 F60 H71 N97 N98 D101 T102 N104 G106 F107 G108 G127 Y131 K145	K12 C14 N16 C18 S44 A46 R47 F53 H64 N90 N91 D94 T95 N97 G99 F100 G101 G120 Y124 K138
BS03	rna	P	N10 M12 Q46 T47 V49 C72 T73 R75 G138 S140 I141 D143 K144 R146 R147 C150 I151 K154 H155	N3 M5 Q39 T40 V42 C65 T66 R68 G131 S133 I134 D136 K137 R139 R140 C143 I144 K147 H148

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006605 protein targeting
• GO:0010628 positive regulation of gene expression
• GO:0032092 positive regulation of protein binding
• GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
• GO:0034504 protein localization to nucleus
• GO:0042273 ribosomal large subunit biogenesis
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdk, PDBe:8jdk, PDBj:8jdk
• PDBsum: 8jdk
• PubMed: 37992713
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)