Structure of PDB 6afz Chain A

Receptor sequence

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

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

3D structure

• PDB: 6afz Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.
• Chain: A
• Resolution: 2.483 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	A	K250 D287 K730 D731	K224 D261 K704 D705
BS02	PO4	A	D253 D507	D227 D481
BS03	MG	A	D253 D257	D227 D231
BS04	MG	A	D253 D727	D227 D701
BS05	MG	A	D283 D507	D257 D481
BS06	MG	A	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:6afz, PDBe:6afz, PDBj:6afz
• PDBsum: 6afz
• PubMed: 30878480
• UniProt: P21616|AVP_VIGRR Pyrophosphate-energized vacuolar membrane proton pump