Structure of PDB 5vp2 Chain 2q Binding Site BS03

Receptor Information
>5vp2 Chain 2q (length=99) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKY
KLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSK
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5vp2 Chain 2q Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D13 E49
Binding residue
(residue number reindexed from 1)		D12 E48
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022627 cytosolic 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:5vp2, PDBe:5vp2, PDBj:5vp2
PDBsum5vp2
PubMed28505372
UniProtP0DOY7|RS17_THET8 Small ribosomal subunit protein uS17 (Gene Name=rpsQ)

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