4hyt

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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium/potassium-transporting ATPase subunit alpha-1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 2 beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside × 1 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside × 1 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 4 O-DODECANYL OCTAETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 2 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 1 O-DODECANYL OCTAETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AT1A1_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1021； UniProt 1–1021 Author chain C； PDBConstruct 1–1021； UniProt 1–1021

Sodium/potassium-transporting ATPase subunit beta-1

OrganismNot specified

UniProt P05027

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 2 beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside × 1 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside × 1 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 4 O-DODECANYL OCTAETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 2 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 1 O-DODECANYL OCTAETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AT1B1_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–303； UniProt 1–303 Author chain D； PDBConstruct 1–303； UniProt 1–303

Na+/K+ ATPase gamma subunit transcript variant a

OrganismNot specified

UniProt Q58K79

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 2 beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside × 1 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside × 1 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 4 O-DODECANYL OCTAETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） MAGNESIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 2 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 1 O-DODECANYL OCTAETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q58K79_PIG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–65； UniProt 1–65 Author chain G； PDBConstruct 1–65； UniProt 1–65

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4hyt
Deposition date deposition_date	2012-11-14
Structure title title	Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site
Keywords keywords	membrane transporter, HYDROLASE-MEMBRANE PROTEIN complex; HYDROLASE/MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4hyt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4hyt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4hyt__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	46.93 Å
Rg (electron density)	47.27 Å
Total Rg	47.03 Å
Atom count	10526
Residues	1314
Excluded volume	189510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4hyt__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4hyt__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Sodium/potassium-transporting ATPase subunit alpha-1
Molecular weight formula_weight	112877.6 kDa
EC 编号 ec_number	3.6.3.9
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	21220

MGKGVGRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNEQLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Entity 2 Entity 2 polymer

Description description	Sodium/potassium-transporting ATPase subunit beta-1
Molecular weight formula_weight	35204.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDDMIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKLNRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPLQYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS

Entity 3 Entity 3 polymer

Description description	Na+/K+ ATPase gamma subunit transcript variant a
Molecular weight formula_weight	7094.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,E

MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPINEDEL

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	OUABAIN
Molecular weight formula_weight	584.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside
Molecular weight formula_weight	496.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside
Molecular weight formula_weight	496.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
Molecular weight formula_weight	788.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 11 Entity 11 non-polymer

Description description	O-DODECANYL OCTAETHYLENE GLYCOL
Molecular weight formula_weight	538.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4hytA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	4hytA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

Domain ID domain_id	4hytA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	4hytA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	4hytB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	4hytB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1660 — Na, k-atpase alpha subunit.

Domain ID domain_id	4hytC01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	4hytC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

Domain ID domain_id	4hytC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	4hytC04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	4hytD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	4hytD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1660 — Na, k-atpase alpha subunit.

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Unit-cell length a length_a	117.470 Å
Unit-cell length b length_b	118.080 Å
Unit-cell length c length_c	494.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.404 Å
Low-resolution limit resolution_low	49.829 Å
R factor r_factor	0.2265
R_work r_work	0.2255
R_free r_free	0.2444

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium/potassium-transporting ATPase subunit alpha-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sodium/potassium-transporting ATPase subunit beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Na+/K+ ATPase gamma subunit transcript variant a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4hyt__assembly_2__model_1

4hyt__assembly_2__model_1 | I(q)

4hyt__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)