Macromolecule Content

Total Structure Weight: 321.40 kDa
Atom Count: 21807
Modelled Residue Count: 2663
Deposited Residue Count: 2768
Unique protein chains: 3

3WGU

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

PDB DOI: 10.2210/pdb3WGU/pdb

Classification: HYDROLASE/TRANSPORT PROTEIN
Organism(s): Sus scrofa
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2013-08-09 Released: 2013-10-09
Deposition Author(s): Kanai, R., Ogawa, H., Vilsen, B., Cornelius, F., Toyoshima, C.

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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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit alpha-1	A, D [auth C]	1016	Sus scrofa	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05024
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit beta-1	B, E [auth D]	303	Sus scrofa	Mutation(s): 0 Gene Names: ATP1B1 Membrane Entity: Yes
UniProt
Find proteins for P05027 (Sus scrofa) Explore P05027 Go to UniProtKB: P05027
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05027
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Na+/K+ ATPase gamma subunit transcript variant a	F [auth E], C [auth G]	65	Sus scrofa	Mutation(s): 0 Gene Names: FXYD2 Membrane Entity: Yes
UniProt
Find proteins for Q58K79 (Sus scrofa) Explore Q58K79 Go to UniProtKB: Q58K79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58K79
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Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth B]	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 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A]	AA [auth C], J [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Ligand Interaction
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain U [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B]	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 Download Ideal Coordinates CCD File SDF format, chain NA [auth D] SDF format, chain W [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain W [auth B]	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 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Y [auth C] MOL2 format, chain H [auth A] MOL2 format, chain Y [auth C]	H [auth A], Y [auth C]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain X [auth C] SDF format, chain Z [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C]	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 SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	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 = 106.383	α = 90
b = 211.6	β = 90
c = 257.124	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Deposited Date: 2013-08-09
Released Date: 2013-10-09

Deposition Author(s):

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

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Deposition Help & Resources

192095 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3WGU

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

Crystal structure of a Na1-bound Na1,K1-ATPase preceding the E1P state

Entity ID: 1

UniProt

Entity Groups

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Entity ID: 2

UniProt

Entity Groups

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Entity ID: 3

UniProt

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)