4HYT

Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site

PDB DOI: https://doi.org/10.2210/pdb4HYT/pdb

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

Deposited: 2012-11-14 Released: 2013-06-26
Deposition Author(s): Laursen, M., Yatime, L., Nissen, P., Fedosova, N.U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.244
R-Value Work: 0.226
R-Value Observed: 0.227

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: 320.76 kDa
Atom Count: 21,220
Modelled Residue Count: 2,632
Deposited Residue Count: 2,778
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]	1,021	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

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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

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

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
17F Query on 17F Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain V [auth G] MOL2 format, chain EA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain V [auth G]	EA [auth D], O [auth A], P [auth A], T [auth B], V [auth G]	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 EA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain V [auth G] Interactions & Density Focus chain EA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain V [auth G]
OBN Query on OBN Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Z [auth C] MOL2 format, chain K [auth A] MOL2 format, chain Z [auth C]	K [auth A], Z [auth C]	OUABAIN C₂₉ H₄₄ O₁₂ LPMXVESGRSUGHW-HBYQJFLCSA-N		Interactions Focus chain K [auth A] Focus chain Z [auth C] Interactions & Density Focus chain K [auth A] Focus chain Z [auth C]
CE1 Query on CE1 Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain Q [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain Q [auth A]	GA [auth E], Q [auth A]	O-DODECANYL OCTAETHYLENE GLYCOL C₂₈ H₅₈ O₉ YYELLDKEOUKVIQ-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth E] Focus chain Q [auth A]
1DS Query on 1DS Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside C₂₂ H₄₀ O₁₂ DSDLUVQAJPJFTK-AJFJJNJGSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
1AT Query on 1AT Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside C₂₂ H₄₀ O₁₂ STVGXWVWPOLILC-LUQRLMJOSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth E] SDF format, chain L [auth A] SDF format, chain U [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain U [auth G]	AA [auth C], FA [auth E], L [auth A], U [auth G]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth E] Focus chain L [auth A] Focus chain U [auth G] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth E] Focus chain L [auth A] Focus chain U [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain DA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain DA [auth D]	BA [auth D], CA [auth D], DA [auth D], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain R [auth B] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain I [auth A]	H [auth A] I [auth A] J [auth A] W [auth C] X [auth C] H [auth A], I [auth A], J [auth A], W [auth C], X [auth C], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [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
OBN	BindingDB: 4HYT	IC50: min: 1.7, max: 4300 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.244
R-Value Work: 0.226
R-Value Observed: 0.227
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.47	α = 90
b = 118.08	β = 90
c = 494.66	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
RemDAq	data collection
XDS	data reduction
diffraction	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2013-07-17
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

4HYT

Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)