Structure of PDB 6afy Chain B

Receptor sequence

>6afyB (length=740) Species: 3916 (Vigna radiata var. radiata)

GAAILPDLGTEILIPVCAVIGIAFALFQWLLVSKVKLSAVDHNVVVKCAE
IQNAISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFSTSPQACSY
DKTKTCKPALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTTLEAR
KGVGKAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFSA
ITGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAV
IADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLY
PLIVSSVGILVCLLTTLFATDFFEIKAVKEIEPALKKQLVISTVLMTIGV
AVVSFVALPTSFTIFNFGVQKDVKSWQLFLCVAVGLWAGLIIGFVTEYYT
SNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAISIFVSFTF
AAMYGIAVAALGMLSTIATGLAIDAYGPISDNAGGIAEMAGMSHRIRERT
DALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRASITTVDVLTPKVF
IGLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPD
YATCVKISTDASIKEMIPPGALVMLTPLVVGILFGVETLSGVLAGSLVSG
VQIAISASNTGGAWDNAKKYIEAGASEHARSLGPKGSDCHKAAVIGDTIG
DPLKDTSGPSLNILIKLMAVESLVFAPFFATHGGLLFKIF

3D structure

• PDB: 6afy Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.
• Chain: B
• Resolution: 2.401 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	K250 D287 D731	K224 D261 D705
BS02	PO4	B	D253 D507	D227 D481
BS03	MG	B	D253 D257	D227 D231
BS04	MG	B	D253 D727	D227 D701
BS05	MG	B	D283 D507	D257 D481
BS06	MG	B	N534 D691	N508 D665

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:6afy, PDBe:6afy, PDBj:6afy
• PDBsum: 6afy
• PubMed: 30878480
• UniProt: P21616|AVP_VIGRR Pyrophosphate-energized vacuolar membrane proton pump