Structure of PDB 6afs Chain B Binding Site BS06

Receptor Information
>6afs Chain B (length=739) Species: 3916 (Vigna radiata var. radiata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAAILPDLGTEILIPVCAVIGIAFALFQWLLVSKVKLSADHNVVVKCAEI
QNAISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFSTSPQACSYD
KTKTCKPALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTTLEARK
GVGKAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFEAI
TGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAVI
ADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLYP
LIVSSVGILVCLLTTLFATDFFEIKAVKEIEPALKKQLVISTVLMTIGVA
VVSFVALPTSFTIFNFGVQKDVKSWQLFLCVAVGLWAGLIIGFVTEYYTS
NAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAISIFVSFTFA
AMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTD
ALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRASITTVDVLTPKVFI
GLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPDY
ATCVKISTDASIKEMIPPGALVMLTPLVVGILFGVETLSGVLAGSLVSGV
QIAISASNTGGAWDNAKKYIEAGASEHARSLGPKGSDCHKAAVIGDTIGD
PLKDTSGPSLNILIKLMAVESLVFAPFFATHGGLLFKIF
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 chain6afs Chain B Residue 1007 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6afs Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.
Resolution2.299 Å
Binding residue
(original residue number in PDB)		N534 D691
Binding residue
(residue number reindexed from 1)		N507 D664
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.3.1: H(+)-exporting diphosphatase.
Gene Ontology
Molecular Function
GO:0004427 inorganic diphosphate phosphatase activity
GO:0009678 diphosphate hydrolysis-driven proton transmembrane transporter activity
GO:0046872 metal ion binding
Biological Process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005773 vacuole
GO:0005774 vacuolar membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6afs, PDBe:6afs, PDBj:6afs
PDBsum6afs
PubMed30878480
UniProtP21616|AVP_VIGRR Pyrophosphate-energized vacuolar membrane proton pump

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