4RET

Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium

PDB DOI: https://doi.org/10.2210/pdb4RET/pdb

Classification: MEMBRANE PROTEIN, HYDROLASE/INHIBITOR
Organism(s): Sus scrofa
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2014-09-23 Released: 2015-01-28
Deposition Author(s): Gregersen, J.L., Laursen, M., Yatime, L., Nissen, P., Fedosova, N.U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.253
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 317.96 kDa
Atom Count: 21,123
Modelled Residue Count: 2,634
Deposited Residue Count: 2,778
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]	1,021	Sus scrofa	Mutation(s): 0 EC: 3.6.3.9 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

Oligosaccharides

Help

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	G [auth F]	2		N-Glycosylation	Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	H, I	2		N/A	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
17F Query on 17F Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B]	O [auth A], P [auth A], R [auth B]	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine C₄₂ H₇₈ N O₁₀ P WTBFLCSPLLEDEM-JIDRGYQWSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B]
DGX Query on DGX Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain X [auth C] MOL2 format, chain N [auth A] MOL2 format, chain X [auth C]	N [auth A], X [auth C]	DIGOXIN C₄₁ H₆₄ O₁₄ LTMHDMANZUZIPE-PUGKRICDSA-N		Interactions Focus chain N [auth A] Focus chain X [auth C] Interactions & Density Focus chain N [auth A] Focus chain X [auth C]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth G] SDF format, chain W [auth C] SDF format, chain Y [auth C] MOL2 format, chain M [auth A] MOL2 format, chain S [auth G] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C]	M [auth A], S [auth G], W [auth C], Y [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain M [auth A] Focus chain S [auth G] Focus chain W [auth C] Focus chain Y [auth C] Interactions & Density Focus chain M [auth A] Focus chain S [auth G] Focus chain W [auth C] Focus chain Y [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain AA [auth D] SDF format, chain Q [auth B] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth D]	AA [auth D], BA [auth D], Q [auth B], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain Q [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain Q [auth B] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	J [auth A] K [auth A] L [auth A] T [auth C] U [auth C] J [auth A], K [auth A], L [auth A], T [auth C], U [auth C], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD Query on PHD	A, D [auth C]	L-PEPTIDE LINKING	C₄ H₈ N O₇ P		ASP

Binding Affinity Annotations
ID	Source	Binding Affinity
DGX	BindingDB: 4RET	IC50: min: 5.5, max: 500 (nM) from 3 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	H, I	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.253
R-Value Work: 0.221
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.24	α = 90
b = 118.35	β = 90
c = 494.09	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Diffraction	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2015-02-11
Changes: Database references
Version 1.2: 2015-02-25
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4RET

Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 5

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)