Structure of PDB 6y6x Chain LD

Receptor sequence

>6y6xLD (length=293) Species: 9606 (Homo sapiens) [Search protein sequence]

GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

3D structure

PDB

6y6x Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel.

Chain

Resolution

2.8 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 K8 K10 A11 Y12 R15 Y16 Q17 K19 R23 G26 T28 D29 Y31 R35 L36 Y44 K48 F113 P139 G140 F142 Y145 L150 R152 T153 H175 S176 R179 Q275 D278 R279 Q282 S286 R289 A290	G1 F2 V3 K4 K7 K9 A10 Y11 R14 Y15 Q16 K18 R22 G25 T27 D28 Y30 R34 L35 Y43 K47 F112 P138 G139 F141 Y144 L149 R151 T152 H174 S175 R178 Q274 D277 R278 Q281 S285 R288 A289
BS02	rna	LD	K8 K10 F13 V18 F20 R21 R22 R24 T28 Y30 R33 R50 I52 R54 T56 N57 R58 Q63 I69 E70 D72 M73 I74 Y79 N94 Y95 R152 T155 G156 N157 K158 Y207 Q222 F223 S224 Q225 Y226 Y253 K255 E260 V261 K262 R265 W266 N267 R268 K270 M271 L273 K277 R279 V280 K284	K7 K9 F12 V17 F19 R20 R21 R23 T27 Y29 R32 R49 I51 R53 T55 N56 R57 Q62 I68 E69 D71 M72 I73 Y78 N93 Y94 R151 T154 G155 N156 K157 Y206 Q221 F222 S223 Q224 Y225 Y252 K254 E259 V260 K261 R264 W265 N266 R267 K269 M270 L272 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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:6y6x, PDBe:6y6x, PDBj:6y6x
PDBsum	6y6x
PubMed	32601485
UniProt	P46777\|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)

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