6KPV

Crystal structures of Na+,K+-ATPase in complex with bufalin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report



Literature

X-ray crystal structures of Na+,K+-ATPase in complex with cardiotonic steroids

Ogawa, H.Motoyama, K.Cornelius, F.Vilsen, B.Toyoshima, C.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alphaAC1021Sus scrofaMutation(s): 0 
Gene Names: ATP1A1
EC: 7.2.2.13
Find proteins for P05024 (Sus scrofa)
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Go to UniProtKB:  P05024
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1BD303Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Find proteins for P05027 (Sus scrofa)
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Go to UniProtKB:  P05027
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FXYD domain-containing ion transport regulatorEG65Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I, J
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1AT
Query on 1AT

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A, C
beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside
C22 H40 O12
STVGXWVWPOLILC-LUQRLMJOSA-N
 Ligand Interaction
CLR
Query on CLR

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E, G
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
BUF
Query on BUF

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A, C
bufalin
C24 H34 O4
QEEBRPGZBVVINN-BMPKRDENSA-N
 Ligand Interaction
NAG
Query on NAG

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B, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MG
Query on MG

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

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A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHD
Query on PHD
A,CL-PEPTIDE LINKINGC4 H8 N O7 PASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.792α = 90
b = 118.032β = 90
c = 495.452γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-09-02
    Type: Initial release