Structure of PDB 5gpj Chain B

Receptor sequence

>5gpjB (length=726) Species: 3916 (Vigna radiata var. radiata)

AAILPDLGTEILIPVCAVIGIAFALFQWLLVSKVKLDHNVVVKCAEIQNA
ISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFSTSPQACSYDKTK
TCKPALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTTLEARKGVG
KAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFEAITGY
GLGGSSMALFGRVGGGIYTKAADVGADLVGKDDPRNPAVIADNVGDNVGD
IAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLYPLIVSSVGILV
CLLTTLFATDFFAVKEIEPALKKQLVISTVLMTIGVAVVSFVALPTSFTI
FNFGVQKDVKSWQLFLCVAVGLWAGLIIGFVTEYYTSNAYSPVQDVADSC
RTGAATNVIFGLALGYKSVIIPIFAIAISIFVSFTFAAMYGIAVAALGML
STIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIG
KGFAIGSAALVSLALFGAFVSRASITTVDVLTPKVFIGLIVGAMLPYWFS
AMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPDYATCVKISTDASIK
EMIPPGALVMLTPLVVGILFGVETLSGVLAGSLVSGVQIAISASNTGGAW
DNAKKYIEAGASEHARSLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNIL
IKLMAVESLVFAPFFATHGGLLFKIF

3D structure

• PDB: 5gpj Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism
• Chain: B
• Resolution: 3.5 Å

Enzymatic activity

• Enzyme Commision number: 7.1.3.1: H(+)-exporting diphosphatase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	PO4	B	D253 D283 D507 K730	D223 D246 D467 K690
BS02	MG	B	D253 D727 K730	D223 D687 K690

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

External links

• PDB: RCSB:5gpj, PDBe:5gpj, PDBj:5gpj
• PDBsum: 5gpj
• PubMed: 27922000
• UniProt: P21616|AVP_VIGRR Pyrophosphate-energized vacuolar membrane proton pump