Structure of PDB 8oj0 Chain LD

Receptor sequence

>8oj0LD (length=293) Species: 9606 (Homo sapiens) [Search protein sequence]

GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

3D structure

PDB

8oj0 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER

Chain

Resolution

3.3 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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	G2 F3 V4 K5 K10 A11 R15 Y16 Q17 K19 R23 T28 D29 R35 L36 Y44 K48 F113 M115 G140 Y145 L146 L150 R152 T153 F160 P174 H175 S176 K178 R179 R268 S272 A274 Q275 D278 R279 Q282 S286 R289 A290	G1 F2 V3 K4 K9 A10 R14 Y15 Q16 K18 R22 T27 D28 R34 L35 Y43 K47 F112 M114 G139 Y144 L145 L149 R151 T152 F159 P173 H174 S175 K177 R178 R267 S271 A273 Q274 D277 R278 Q281 S285 R288 A289
BS02	rna	LD	K8 K10 F13 K14 V18 F20 R21 R22 R24 T28 Y30 R33 R50 I52 R54 T56 N57 R58 I61 Q63 I69 E70 D72 I74 N94 R152 T154 T155 K158 H198 V204 Y207 K221 Q222 F223 S224 Q225 Y226 Y253 K255 K256 K258 K259 V261 K262 W266 N267 R268 K270 M271 L273 K276 K277 R279 V280	K7 K9 F12 K13 V17 F19 R20 R21 R23 T27 Y29 R32 R49 I51 R53 T55 N56 R57 I60 Q62 I68 E69 D71 I73 N93 R151 T153 T154 K157 H197 V203 Y206 K220 Q221 F222 S223 Q224 Y225 Y252 K254 K255 K257 K258 V260 K261 W265 N266 R267 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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8oj0, PDBe:8oj0, PDBj:8oj0
PDBsum	8oj0
PubMed	38383785
UniProt	P46777\|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)

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