6JXK

Rb+-bound E2-MgF state of the gastric proton pump (Wild-type)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A single K+-binding site in the crystal structure of the gastric proton pump

Yamamoto, K.Dubey, V.Irie, K.Nakanishi, H.Khandelia, H.Fujiyoshi, Y.Abe, K.

(2019) Elife --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase alpha chain 1
A, E
987Sus scrofaMutation(s): 3 
Gene Names: ATP4A
EC: 7.2.2.19
Find proteins for P19156 (Sus scrofa)
Go to Gene View: ATP4A
Go to UniProtKB:  P19156
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase subunit beta
B, F
289Sus scrofaMutation(s): 0 
Gene Names: ATP4B
Find proteins for P18434 (Sus scrofa)
Go to Gene View: ATP4B
Go to UniProtKB:  P18434
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MF4
Query on MF4

Download SDF File 
Download CCD File 
A, E
TETRAFLUOROMAGNESATE(2-)
MAGNESIUMTETRAFLUORIDE
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A, F
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 191.510α = 90.00
b = 106.430β = 107.79
c = 250.960γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release