Structure of PDB 8y0w Chain LD Binding Site BS02

Receptor Information
>8y0w 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
>8y0w 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
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PDB8y0w dormant ribosome with eIF5A, eEF2 and SERBP1
Resolution3.4 Å
Binding residue
(original residue number in PDB)		F13 K14 V18 F20 R21 R22 R24 T28 Y30 R33 R50 R54 T56 N57 R58 Q63 I69 D72 M73 I74 N94 R152 T155 K158 Y207 Q222 S224 Q225 Y253 E260 V261 K262 K263 R265 W266 N267 R268 K270 M271 K276 K277 R279 V280
Binding residue
(residue number reindexed from 1)		F12 K13 V17 F19 R20 R21 R23 T27 Y29 R32 R49 R53 T55 N56 R57 Q62 I68 D71 M72 I73 N93 R151 T154 K157 Y206 Q221 S223 Q224 Y252 E259 V260 K261 K262 R264 W265 N266 R267 K269 M270 K275 K276 R278 V279
Enzymatic activity
Enzyme Commision number ?
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
PDBsum8y0w
PubMed38698775
UniProtP46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)

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