7d93

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)

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 2	Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） FXYD domain-containing ion transport regulator × 1 （Q58K79） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAGNESIUM ION × 2 SODIUM ION × 1 CHOLESTEROL × 3 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ;[(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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 2	Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） FXYD domain-containing ion transport regulator × 1 （Q58K79） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAGNESIUM ION × 2 SODIUM ION × 1 CHOLESTEROL × 2 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 ;[(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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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 1–1016； UniProt 6–1021 Author chain C； PDBConstruct 1–1016； UniProt 6–1021

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 2	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） FXYD domain-containing ion transport regulator × 1 （Q58K79） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAGNESIUM ION × 2 SODIUM ION × 1 CHOLESTEROL × 3 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ;[(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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 2	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） FXYD domain-containing ion transport regulator × 1 （Q58K79） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAGNESIUM ION × 2 SODIUM ION × 1 CHOLESTEROL × 2 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 ;[(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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

FXYD domain-containing ion transport regulator

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 2	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 × 2 MAGNESIUM ION × 2 SODIUM ION × 1 CHOLESTEROL × 3 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ;[(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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 2	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 × 2 MAGNESIUM ION × 2 SODIUM ION × 1 CHOLESTEROL × 2 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 ;[(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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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	7d93
Deposition date deposition_date	2020-10-12
Structure title title	Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)
Keywords keywords	Na+, K+-ATPase, membrane protein, ion transport, Cardiotonic steroids, TRANSPORT PROTEIN; TRANSPORT 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.

7d93__assembly_1__model_1

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

Download this curve (.dat)

7d93__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d93__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.77 Å
Rg (electron density)	47.08 Å
Total Rg	46.80 Å
Atom count	10695
Residues	1318
Excluded volume	192720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d93__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7d93__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 (11)

Entity 1 Entity 1 polymer

Description description	Sodium/potassium-transporting ATPase subunit alpha-1
Molecular weight formula_weight	112403.9 kDa
EC 编号 ec_number	7.2.2.13
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	21396

GRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNEQLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

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	FXYD domain-containing ion transport regulator
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	E,G

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	4

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	4

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	5

Entity 8 Entity 8 non-polymer

Description description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	787.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 9 Entity 9 non-polymer

Description description	;[(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 ;
Molecular weight formula_weight	788.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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Unit-cell length a length_a	115.620 Å
Unit-cell length b length_b	117.890 Å
Unit-cell length c length_c	494.300 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	orthorhombic

Resolution resolution	3.650 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2355
R_work r_work	0.2334
R_free r_free	0.2742

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)

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

Sodium/potassium-transporting ATPase subunit beta-1

State in the Current Structure

Other States of the Same Protein in the Database

FXYD domain-containing ion transport regulator

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7d93__assembly_1__model_1

7d93__assembly_1__model_1 | I(q)

7d93__assembly_1__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 (11)

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 water

7. Citations (1)

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)

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

FXYD domain-containing ion transport regulator

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

7d93__assembly_1__model_1

7d93__assembly_1__model_1 | I(q)

7d93__assembly_1__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 (11)

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 water

7. Citations (1)