Structure of PDB 5vp2 Chain 2U Binding Site BS04

Receptor Information

>5vp2 Chain 2U (length=116) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQ

Ligand information

InChI=1S/Mg/q+2

JLVVSXFLKOJNIY-UHFFFAOYSA-N

SMILES

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

Formula

Mg

Name

MAGNESIUM ION

PDB chain

5vp2 Chain 2U Residue 205 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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PDB	5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
Resolution	2.8 Å
Binding residue (original residue number in PDB)	G7 V8 V9 R10 R11
Binding residue (residue number reindexed from 1)	G6 V7 V8 R9 R10
Annotation score	4

Enzymatic activity

Enzyme Commision number

Gene Ontology

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

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

	Cellular Component
GO:0005840	ribosome
GO:0022625	cytosolic large ribosomal subunit
GO:1990904	ribonucleoprotein complex

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External links

PDB	RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
PDBsum	5vp2
PubMed	28505372
UniProt	P60491\|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)

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