3WGV

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin

PDB DOI: https://doi.org/10.2210/pdb3WGV/pdb

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

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: 0.298
R-Value Work: 0.270
R-Value Observed: 0.270

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 322.98 kDa
Atom Count: 21,909
Modelled Residue Count: 2,663
Deposited Residue Count: 2,768
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(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]	1,016	Sus scrofa	Mutation(s): 0 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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(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 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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Na+/K+ ATPase gamma subunit transcript variant a	C [auth G], F [auth E]	65	Sus scrofa	Mutation(s): 0 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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EFO Query on EFO Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain KA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain KA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain KA [auth C]	KA [auth C], U [auth A]	Oligomycin A C₄₅ H₇₄ O₁₁ MNULEGDCPYONBU-AWJDAWNUSA-N		Interactions Focus chain KA [auth C] Focus chain U [auth A]
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth C] 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] SDF format, chain IA [auth C] SDF format, chain NA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] 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] MOL2 format, chain IA [auth C] MOL2 format, chain NA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain NA [auth D]	GA [auth C] HA [auth C] IA [auth C] JA [auth C] NA [auth D] GA [auth C], HA [auth C], IA [auth C], JA [auth C], NA [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		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth B]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain J [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain J [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain J [auth A]	BA [auth C], J [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain J [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain X [auth G] SDF format, chain LA [auth D] SDF format, chain MA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain X [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain X [auth G] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D]	LA [auth D] MA [auth D] O [auth A] P [auth A] PA [auth E] LA [auth D], MA [auth D], O [auth A], P [auth A], PA [auth E], X [auth G]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain LA [auth D] Focus chain MA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth E] Focus chain X [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain W [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain W [auth B]	OA [auth D], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain OA [auth D] Focus chain W [auth B]
ALF Query on ALF Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain H [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain H [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain H [auth A]	H [auth A], Z [auth C]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain H [auth A] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain AA [auth C] SDF format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain Y [auth C]	AA [auth C], G [auth A], I [auth A], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain L [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] K [auth A] CA [auth C], DA [auth C], EA [auth C], FA [auth C], K [auth A], L [auth A], M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.298
R-Value Work: 0.270
R-Value Observed: 0.270
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.285	α = 90
b = 210.183	β = 90
c = 256.086	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

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