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 1.2 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-1A,
D [auth C]
1016Sus scrofaMutation(s): 0 
Gene Names: ATP1A1
EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P05024 (Sus scrofa)
Explore P05024 
Go to UniProtKB:  P05024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05024
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1B,
E [auth D]
303Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Membrane Entity: Yes 
UniProt
Find proteins for P05027 (Sus scrofa)
Explore P05027 
Go to UniProtKB:  P05027
Entity Groups  
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UniProt GroupP05027
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Na+/K+ ATPase gamma subunit transcript variant aF [auth E],
C [auth G]
65Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane Entity: Yes 
UniProt
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58K79
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth D],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth D],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
V [auth B]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
ADP
Query on ADP

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AA [auth C],
J [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CLR
Query on CLR

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FA [auth C],
GA [auth C],
HA [auth C],
O [auth A],
P [auth A],
FA [auth C],
GA [auth C],
HA [auth C],
O [auth A],
P [auth A],
U [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
NAG
Query on NAG

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NA [auth D],
W [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ALF
Query on ALF

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H [auth A],
Y [auth C]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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G [auth A],
I [auth A],
X [auth C],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
K [auth A],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
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  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary