Structure of PDB 8xsx Chain LY

Receptor sequence

>8xsxLY (length=134) Species: 9606 (Homo sapiens)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

3D structure

• PDB: 8xsx Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LY
• Resolution: 2.4 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	LY	M1 K2 F3 N4 P5 F6 T8 S9 R11 K13 N14 R15 R17 H18 K28 S31 P33 K36 R45 S46 R59 G60 H61 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 V128 K132	M1 K2 F3 N4 P5 F6 T8 S9 R11 K13 N14 R15 R17 H18 K28 S31 P33 K36 R45 S46 R59 G60 H61 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 V128 K132
BS02	rna	LY	R11 R15 K16 F19 N20 P22 S23 H24 R27 R50 K51 Q72 V73 Y74 R75 K76 D112 D114 I118	R11 R15 K16 F19 N20 P22 S23 H24 R27 R50 K51 Q72 V73 Y74 R75 K76 D112 D114 I118

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• 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:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xsx, PDBe:8xsx, PDBj:8xsx
• PDBsum: 8xsx
• PubMed: 38942792
• UniProt: P61254|RL26_HUMAN Large ribosomal subunit protein uL24 (Gene Name=RPL26)