1Q3I | pdb_00001q3i

Crystal Structure of Na,K-ATPase N-domain

• PDB DOI: https://doi.org/10.2210/pdb1Q3I/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-07-30 Released: 2004-08-03 
• Deposition Author(s): Hakansson, K.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.292 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.254 (DCC) 

Literature

The Crystallographic Structure of Na,K-ATPase N-domain at 2.6 A Resolution

Hakansson, K.O.

(2003) J Mol Biology 332: 1175-1182

• PubMed: 14499619 
• DOI: https://doi.org/10.1016/j.jmb.2003.07.012
• Primary Citation Related Structures: 
  1Q3I


• PubMed Abstract: 
  

  The structure of the N-domain of porcine alpha(2) Na,K-ATPase was determined crystallographically to 3.2A resolution by isomorphous heavy-atom replacement using a single mercury derivative. The structure was finally refined against 2.6A resolution synchrotron data. The domain forms a seven-stranded antiparallel beta-sheet with two additional beta-strands forming a hairpin and five alpha-helices. Approximately 75% of the residues were superimposable with residues from the structure of Ca-ATPase N-domain, and a structure-based sequence alignment is presented. The positions of key residues are discussed in relation to the pattern of hydrophobicity, charge and sequence conservation of the molecular surface. The structure of a hexahistidine tag binding to nickel ions is presented.

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Organizational Affiliation: 
• August Krogh Institute, Copenhagen University, Universitetsparken 13, DK-2100 OE, Copenhagen, Denmark. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 24.3 kDa 
• Atom Count: 1,612 
• Modeled Residue Count: 192 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na,K-ATPase	A	214	Sus scrofa	Mutation(s): 0  EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
UniProt
Find proteins for D2WKD8 (Sus scrofa) Explore D2WKD8  Go to UniProtKB:  D2WKD8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A], C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.292 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.254 (DCC) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.31	α = 90
b = 147.31	β = 90
c = 147.31	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-03 
Deposition Author(s): Hakansson, K.O.

Revision History  

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2018-03-07
  Changes: Data collection
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations