Structure of PDB 8k2c Chain LD Binding Site BS02

Receptor Information
>8k2c Chain LD (length=293) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA
Ligand information
>8k2c Chain L7 (length=120) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gucuacggccauaccacccugaacgcgcccgaucucgucugaucucggaa
gcuaagcagggucgggccugguuaguacuuggaugggagaccgccuggga
auaccgggugcuguaggcuu
<<<<<<<<<....<<<<<<<<.....<<<<<..............>>>..
>>....>>>>>>.>><<<<<<<.....<<.<<..<<....>>.>>.>>..
..>>>>>>>>>>>>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8k2c Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		K8 K10 F13 K14 V18 F20 R21 R22 R24 K27 T28 Y30 R33 R50 I52 R54 T56 N57 R58 I61 Q63 I69 E70 G71 D72 M73 I74 N94 Y95 R152 T154 T155 G156 N157 K158 H198 Y207 Y210 Q222 F223 S224 Q225 Y226 Y253 K255 K258 E260 V261 K262 K263 W266 N267 R268 P269 K270 M271 L273 K276 K277 R279 V280 K284
Binding residue
(residue number reindexed from 1)		K7 K9 F12 K13 V17 F19 R20 R21 R23 K26 T27 Y29 R32 R49 I51 R53 T55 N56 R57 I60 Q62 I68 E69 G70 D71 M72 I73 N93 Y94 R151 T153 T154 G155 N156 K157 H197 Y206 Y209 Q221 F222 S223 Q224 Y225 Y252 K254 K257 E259 V260 K261 K262 W265 N266 R267 P268 K269 M270 L272 K275 K276 R278 V279 K283
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8k2c, PDBe:8k2c, PDBj:8k2c
PDBsum8k2c
PubMed38942792
UniProtP46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)

[Back to BioLiP]