7D92

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P4(3)2(1)2 symmetry)

PDB DOI: https://doi.org/10.2210/pdb7D92/pdb

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

Deposited: 2020-10-12 Released: 2021-01-27
Deposition Author(s): Kanai, R., Cornelius, F., Ogawa, H., Motoyama, K., Vilsen, B., Toyoshima, C.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Danish Council for Independent Research, Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.257
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 163.65 kDa
Atom Count: 10,740
Modelled Residue Count: 1,319
Deposited Residue Count: 1,384
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	1,016	Sus scrofa	Mutation(s): 0 EC: 7.2.2.13 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	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
FXYD domain-containing ion transport regulator	C [auth G]	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

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H0C (Subject of Investigation/LOI) Query on H0C Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A]	Q [auth A]	[(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S},5~{S},8~{R},9~{S},10~{R},11~{R},13~{R},14~{S},17~{R})-10-(hydroxymethyl)-13-methyl-1,5,11,14-tetrakis(oxidanyl)-17-(5-oxidanylidene-2~{H}-furan-3-yl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-6-methyl-3,5-bis(oxidanyl)oxan-4-yl] anthracene-9-carboxylate C₄₄ H₅₂ O₁₃ CSNRMZGUGASWCS-XLAOFTCCSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
PCW Query on PCW Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain T [auth G] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth G]	H [auth A], R [auth B], T [auth G]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth A] Focus chain R [auth B] Focus chain T [auth G] Interactions & Density Focus chain H [auth A] Focus chain R [auth B] Focus chain T [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B]	S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BFD Query on BFD	A	L-PEPTIDE LINKING	C₄ H₆ Be F₃ N O₄		ASP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.257
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.234	α = 90
b = 84.234	β = 90
c = 646.262	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
DENZO	data reduction
SCALEPACK	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16K18500
Japan Society for the Promotion of Science (JSPS)	Japan	16H02499
Japan Society for the Promotion of Science (JSPS)	Japan	19H00975
Danish Council for Independent Research	Denmark	DFF7016-00193B
Danish Council for Independent Research	Denmark	DFF4183-00011A
Novo Nordisk Foundation	Denmark	NNF13OC0013409
Novo Nordisk Foundation	Denmark	NNF13OC0006555