3WGU

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state without oligomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a Na1-bound Na1,K1-ATPase preceding the E1P state

Kanai, R.Ogawa, H.Vilsen, B.Cornelius, F.Toyoshima, C.

(2013) Nature 502: 201-206


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit alpha-1
A, C
1016Sus scrofaMutation(s): 0 
Gene Names: ATP1A1
EC: 7.2.2.13
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for P05024 (Sus scrofa)
Go to Gene View: ATP1A1
Go to UniProtKB:  P05024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit beta-1
B, D
303Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for P05027 (Sus scrofa)
Go to Gene View: ATP1B1
Go to UniProtKB:  P05027
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Na+/K+ ATPase gamma subunit transcript variant a
G, E
65Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for Q58K79 (Sus scrofa)
Go to Gene View: FXYD2
Go to UniProtKB:  Q58K79
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PC1
Query on PC1

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Download CCD File 
A, B, C, D
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
ALF
Query on ALF

Download SDF File 
Download CCD File 
A, C
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.383α = 90.00
b = 211.600β = 90.00
c = 257.124γ = 90.00
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references