Structure of PDB 5doy Chain 1d Binding Site BS03

Receptor Information

>5doy Chain 1d (length=208) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

Ligand information

Ligand ID

InChI

InChI=1S/Mg/q+2

InChIKey

JLVVSXFLKOJNIY-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Mg+2]
CACTVS 3.341	[Mg++]

Formula

Name

MAGNESIUM ION

PDB chain

5doy Chain 1d Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5doy Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.
Resolution	2.6 Å
Binding residue (original residue number in PDB)	S83 K85 T89
Binding residue (residue number reindexed from 1)	S82 K84 T88
Annotation score	4

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0019843	rRNA binding
GO:0046872	metal ion binding

	Biological Process
GO:0006412	translation
GO:0042274	ribosomal small subunit biogenesis

	Cellular Component
GO:0005840	ribosome
GO:0015935	small 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:5doy, PDBe:5doy, PDBj:5doy
PDBsum	5doy
PubMed	26028538
UniProt	P80373\|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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