Structure of PDB 5gpj Chain B Binding Site BS02

Receptor Information
>5gpj Chain B (length=726) Species: 3916 (Vigna radiata var. radiata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAILPDLGTEILIPVCAVIGIAFALFQWLLVSKVKLDHNVVVKCAEIQNA
ISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFSTSPQACSYDKTK
TCKPALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTTLEARKGVG
KAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFEAITGY
GLGGSSMALFGRVGGGIYTKAADVGADLVGKDDPRNPAVIADNVGDNVGD
IAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLYPLIVSSVGILV
CLLTTLFATDFFAVKEIEPALKKQLVISTVLMTIGVAVVSFVALPTSFTI
FNFGVQKDVKSWQLFLCVAVGLWAGLIIGFVTEYYTSNAYSPVQDVADSC
RTGAATNVIFGLALGYKSVIIPIFAIAISIFVSFTFAAMYGIAVAALGML
STIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIG
KGFAIGSAALVSLALFGAFVSRASITTVDVLTPKVFIGLIVGAMLPYWFS
AMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPDYATCVKISTDASIK
EMIPPGALVMLTPLVVGILFGVETLSGVLAGSLVSGVQIAISASNTGGAW
DNAKKYIEAGASEHARSLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNIL
IKLMAVESLVFAPFFATHGGLLFKIF
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 chain5gpj Chain B Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5gpj Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism
Resolution3.5 Å
Binding residue
(original residue number in PDB)		D253 D727 K730
Binding residue
(residue number reindexed from 1)		D223 D687 K690
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5gpj, PDBe:5gpj, PDBj:5gpj
PDBsum5gpj
PubMed27922000
UniProtP21616|AVP_VIGRR Pyrophosphate-energized vacuolar membrane proton pump

[Back to BioLiP]