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 1.3 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

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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]	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

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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

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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	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 KA [auth C] SDF format, chain U [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain U [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain U [auth A]	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] Interactions & Density 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 IA [auth C] SDF format, chain JA [auth C] SDF format, chain NA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain V [auth B] SDF format, chain HA [auth C] SDF format, chain S [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain S [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain NA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain S [auth A]	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] Interactions & Density 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] Interactions & Density Focus chain BA [auth C] Focus chain J [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain X [auth G] MOL2 format, chain LA [auth D] MOL2 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] mmCIF format, chain LA [auth D] mmCIF 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]	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] Interactions & Density 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] Interactions & Density Focus chain OA [auth D] Focus chain W [auth B]
ALF Query on ALF Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Z [auth C] MOL2 format, chain H [auth A] MOL2 format, chain Z [auth C] mmCIF format, chain H [auth A] mmCIF format, chain Z [auth C]	H [auth A], Z [auth C]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain H [auth A] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain Y [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] 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] Interactions & Density 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] Interactions & Density 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

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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
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary