3KDP

Crystal structure of the sodium-potassium pump

Structural Biology Knowledgebase: 3KDP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.242

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KDP

Classification: HYDROLASE

Total Structure Weight: 294290.93

Macromolecule Entities
Molecule Chains Length Organism Details
Sodium/potassium-transporting ATPase subunit alpha-1 A, C 998 Sus scrofa EC#: 3.6.3.9 IUBMB
Fragment: ALPHA chain (UNP RESIDUES 24-1021)
Gene Name(s): ATP1A1 Gene View
Sodium/potassium-transporting ATPase subunit beta-1 B, D 286 Sus scrofa Fragment: BETA chain (UNP RESIDUES 18-303)
Mutation: F151S
Gene Name(s): ATP1B1 Gene View
Na+/K+ ATPase gamma subunit transcript variant a G, H 27 Sus scrofa Fragment: GAMMA chain (UNP RESIDUES 23-49)
Mutation: I45L
Gene Name(s): FXYD2 Gene View

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: P-type ATPase

Protein Name: Na,K-ATPase; pig kidney


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLR
Query on CLR

B, D CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MF4
Query on MF4

A, C TETRAFLUOROMAGNESATE(2-)
MAGNESIUMTETRAFLUORIDE (Synonym)
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RB
Query on RB

A, C RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.242
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.93 α = 90.00
b = 261.50 β = 90.00
c = 334.78 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-23
  • Released Date: 2010-02-16
  • Deposition author(s): Morth, J.P., Pedersen, B.P., Nissen, P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4