Structure of PDB 5ndw Chain M1

Receptor sequence

>5ndwM1 (length=169) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

3D structure

PDB

5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.

Chain

Resolution

3.7 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	M1	K16 V18 N20 S22 G24 S48 A50 R51 Y52 F57 I65 H68 N95 S97 A98 T99 N101 G103 F104 G105 G124 M125 D126 Y128 K142 K174	K11 V13 N15 S17 G19 S43 A45 R46 Y47 F52 I60 H63 N90 S92 A93 T94 N96 G98 F99 G100 G119 M120 D121 Y123 K137 K169
BS02	rna	M1	Q43 T44 V46 V69 T70 R72 G135 R137 V138 R140 R141 R143 V148 G149 N150 H152	Q38 T39 V41 V64 T65 R67 G130 R132 V133 R135 R136 R138 V143 G144 N145 H147

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0019843	rRNA binding

	Biological Process
GO:0000027	ribosomal large subunit assembly
GO:0002181	cytoplasmic translation
GO:0006412	translation

	Cellular Component
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005840	ribosome
GO:0022625	cytosolic large ribosomal subunit
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:5ndw, PDBe:5ndw, PDBj:5ndw
PDBsum	5ndw
PubMed	29208708
UniProt	Q3E757\|RL11B_YEAST Large ribosomal subunit protein uL5B (Gene Name=RPL11B)

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