Structure of PDB 8xsy Chain LL

Receptor sequence

>8xsyLL (length=210) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDVEKKK

3D structure

• PDB: 8xsy Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LL
• Resolution: 3.0 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	LL	A2 S4 R5 M8 L10 K11 P12 H13 F14 H15 K16 W18 W25 Q28 P29 R31 K32 R35 R36 R39 K42 R44 R56 V59 R60 P62 T63 Y66 H67 R71 R74 L78 R92 D99 P100 R101 R102 R103 K105 S106 R129 K130 S132 K135 R158 N159 K165 F179 R183 R186 A187 N188 G193 R195 K197 R198	A1 S3 R4 M7 L9 K10 P11 H12 F13 H14 K15 W17 W24 Q27 P28 R30 K31 R34 R35 R38 K41 R43 R55 V58 R59 P61 T62 Y65 H66 R70 R73 L77 R91 D98 P99 R100 R101 R102 K104 S105 R128 K129 S131 K134 R157 N158 K164 F178 R182 R185 A186 N187 G192 R194 K196 R197
BS02	rna	LL	F26 N27 A30 R34	F25 N26 A29 R33

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xsy, PDBe:8xsy, PDBj:8xsy
• PDBsum: 8xsy
• PubMed: 38942792
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)