3WGU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 

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: 3.6.3.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase with bound Na+ preceding the E1P state
Find proteins for I7HD36 (Sus scrofa)
Go to UniProtKB:  I7HD36

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit beta-1
B, D
303Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase with bound Na+ preceding the E1P state
Find proteins for P05027 (Sus scrofa)
Go to UniProtKB:  P05027

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Na+/K+ ATPase gamma subunit transcript variant a
E, G
65Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase with bound Na+ preceding the E1P state
Find proteins for Q58K79 (Sus scrofa)
Go to UniProtKB:  Q58K79
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

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

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

Download CCD File 
A, B, C
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
NAG
Query on NAG

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

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

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.383α = 90
b = 211.6β = 90
c = 257.124γ = 90
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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