Structure of PDB 8yop Chain LD

Receptor sequence

>8yopLD (length=293) Species: 9606 (Homo sapiens)

GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

3D structure

• PDB: 8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LD
• 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	LD	F3 V4 K5 K8 A11 Y12 R15 Y16 Q17 K19 R23 G26 T28 D29 Y31 R35 L36 K43 Y44 K48 F113 M115 G140 F142 Y145 R152 T153 F160 P174 H175 S176 R179 R268 A274 Q275 D278 R279 Q282 S286 R289	F2 V3 K4 K7 A10 Y11 R14 Y15 Q16 K18 R22 G25 T27 D28 Y30 R34 L35 K42 Y43 K47 F112 M114 G139 F141 Y144 R151 T152 F159 P173 H174 S175 R178 R267 A273 Q274 D277 R278 Q281 S285 R288
BS02	rna	LD	K8 K10 F13 K14 Y16 V18 F20 R21 R22 R24 T28 Y30 R33 R50 I52 R54 T56 N57 R58 I61 Q63 I69 E70 D72 M73 I74 N94 R152 T155 G156 N157 K158 H198 V204 Y207 Y210 Q222 F223 S224 Q225 Y226 Y253 K255 K258 E260 V261 K262 K263 K264 R265 W266 N267 R268 P269 K270 M271 L273 K276 K277 R279 V280	K7 K9 F12 K13 Y15 V17 F19 R20 R21 R23 T27 Y29 R32 R49 I51 R53 T55 N56 R57 I60 Q62 I68 E69 D71 M72 I73 N93 R151 T154 G155 N156 K157 H197 V203 Y206 Y209 Q221 F222 S223 Q224 Y225 Y252 K254 K257 E259 V260 K261 K262 K263 R264 W265 N266 R267 P268 K269 M270 L272 K275 K276 R278 V279

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003730 mRNA 3'-UTR 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:0048027 mRNA 5'-UTR 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:0010628 positive regulation of gene expression
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0050821 protein stabilization
• GO:1901796 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:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• 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: P46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)