Structure of PDB 8ud6 Chain 2d Binding Site BS02

Receptor Information

>8ud6 Chain 2d (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

8ud6 Chain 2d Residue 301 [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	8ud6 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
Resolution	2.7 Å
Binding residue (original residue number in PDB)	A82 S83 K85 T89
Binding residue (residue number reindexed from 1)	A81 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:8ud6, PDBe:8ud6, PDBj:8ud6
PDBsum	8ud6
PubMed	38359125
UniProt	P80373\|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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