Structure of PDB 8yop Chain LJ

Receptor sequence

>8yopLJ (length=176) Species: 9606 (Homo sapiens)

QDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSK
ARYTVRSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDT
GNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIG
AKHRISKEEAMRWFQQKYDGIILPGK

3D structure

• PDB: 8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LJ
• Resolution: 2.2 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	LJ	K19 C21 N23 C25 S51 A53 R54 F60 I62 A69 N97 N98 S100 D101 T102 N104 G106 F107 G108 G127 D129 Y131 V133 K145	K17 C19 N21 C23 S49 A51 R52 F58 I60 A67 N95 N96 S98 D99 T100 N102 G104 F105 G106 G125 D127 Y129 V131 K143
BS02	rna	LJ	M12 R13 R16 Q46 T47 V49 T73 R75 G138 S140 I141 K144 K145 R146 C150 G152 A153 K154 H155 R156	M10 R11 R14 Q44 T45 V47 T71 R73 G136 S138 I139 K142 K143 R144 C148 G150 A151 K152 H153 R154

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:8yop, PDBe:8yop, PDBj:8yop
• PDBsum: 8yop
• PubMed: 38942792
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)