Structure of PDB 8yop Chain SB

Receptor sequence

>8yopSB (length=214) Species: 9606 (Homo sapiens)

VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMME
IMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKK
PKFELGKLMELHGE

3D structure

• PDB: 8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: SB
• 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	SB	K28 K56 S112 V114 K115 K116 W117 Q118 M120 H124 R136 F138 R146 N148 Q149 I150 R151 Y155 Q157 H158 Q159 Q160 R162 R165 S203 I204 Y205 K216	K8 K36 S92 V94 K95 K96 W97 Q98 M100 H104 R116 F118 R126 N128 Q129 I130 R131 Y135 Q137 H138 Q139 Q140 R142 R145 S183 I184 Y185 K196

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:0006412 translation
• GO:0006413 translational initiation
• GO:0030154 cell differentiation
• GO:0042274 ribosomal small subunit biogenesis
• GO:0043066 negative regulation of apoptotic process

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yop, PDBe:8yop, PDBj:8yop
• PDBsum: 8yop
• PubMed: 38942792
• UniProt: P61247|RS3A_HUMAN Small ribosomal subunit protein eS1 (Gene Name=RPS3A)