3a3y

Crystal structure of the sodium-potassium pump with bound potassium and ouabain

Method: X-RAY DIFFRACTION

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

Na, K-ATPase alpha subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	NA+,K+-ATPASE BETA SUBUNIT × 1 Phospholemman-like protein × 1 （Q70Q12） TETRAFLUOROMAGNESATE(2-) × 1 MAGNESIUM ION × 1 POTASSIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4H132_SQUAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1028； UniProt 1–1028

Phospholemman-like protein

OrganismNot specified

UniProt Q70Q12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Na, K-ATPase alpha subunit × 1 （Q4H132） NA+,K+-ATPASE BETA SUBUNIT × 1 TETRAFLUOROMAGNESATE(2-) × 1 MAGNESIUM ION × 1 POTASSIUM ION × 3 OUABAIN × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q70Q12_SQUAC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–74； UniProt 21–94

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	3a3y
Deposition date deposition_date	2009-06-23
Structure title title	Crystal structure of the sodium-potassium pump with bound potassium and ouabain
Keywords keywords	;MEMBRANE PROTEIN, ION PUMP, ATPASE, K+ BINDING, OUABAIN BINDING, HALOACID DEHYDROGENEASE SUPERFAMILY, PHOSPHATE ANALOGUE, ATP-BINDING, HYDROLASE, ION TRANSPORT, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, HYDROLASE-TRANSPORT PROTEIN COMPLEX, Membrane, Transmembrane, Transport ;; HYDROLASE/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.

3a3y__assembly_1__model_1

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

Download this curve (.dat)

3a3y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a3y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.88 Å
Rg (electron density)	47.02 Å
Total Rg	46.78 Å
Atom count	10242
Residues	1295
Excluded volume	184160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a3y__assembly_1__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 (10)

Entity 1 Entity 1 polymer

Description description	Na, K-ATPase alpha subunit
Molecular weight formula_weight	113309.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10308

MGKGTASDKYEPAATSENATKSKKKGKKDKIDKKRDLDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLTPPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLYLGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTINAEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEFSSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGRTPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRAVFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIPFNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLKEDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTTDLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDILHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQWADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMYPLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY

Entity 2 Entity 2 polymer

Description description	NA+,K+-ATPASE BETA SUBUNIT
Molecular weight formula_weight	35175.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MARGKSKETDGGWKKFLWDSEKKEFLGRTGSSWFKIFLFYLIFYGCLAGIFIGTIQVLLLTLSDFEPKYQDRVAPPGLSHAPYAIKTEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPADYIKRGDLDDSQGQKKACRFSRMWLKNCSGLDDTTYGYAEGKPCVVAKLNRIIGFYPKPLKNTTDLPEQLQANYNQYVLPLRCAAKREEDREKIGSIEYFGLGGYAGFPLQYYPYYGKRLQKKYLQPLLAIQFTNLTQNMELRIECKVYGENIDYSEKDRFRGRFEVKIEVKS

Entity 3 Entity 3 polymer

Description description	Phospholemman-like protein
Molecular weight formula_weight	8225.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MDPEGPDNDERFTYDYYRLRVVGLIVAAVLCVIGIIILLAGKCRCKFNQNKRTRSNSGTATAQHLLQPGEATEC

Entity 4 Entity 4 non-polymer

Description description	TETRAFLUOROMAGNESATE(2-)
Molecular weight formula_weight	100.3 kDa
Source method src_method	syn
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	1

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	OUABAIN
Molecular weight formula_weight	584.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 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	3

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3a3ya1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.33 — Metal cation-transporting ATPase, transmembrane domain
Superfamily Superfamily superfamily	f.33.1 — Metal cation-transporting ATPase, transmembrane domain
Family Family family	f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain

Domain ID domain_id	d3a3ya2
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.7 — Metal cation-transporting ATPase, actuator domain A
Family Family family	b.82.7.1 — Metal cation-transporting ATPase, actuator domain A

Domain ID domain_id	d3a3ya3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.7 — Meta-cation ATPase, catalytic domain P

Domain ID domain_id	d3a3ya4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

Domain ID domain_id	d3a3yb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.42 — Sodium/potassium-transporting ATPase, beta subunit transmembrane helix
Family Family family	f.23.42.0 — automated matches

Domain ID domain_id	d3a3yb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.32 — Sodium/potassium-transporting ATPase, beta subunit extracellular domain
Family Family family	b.1.32.1 — Sodium/potassium-transporting ATPase, beta subunit extracellular domain

Domain ID domain_id	d3a3yg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.43 — ATP1G1/PLM/MAT8-like (FXYD-like)
Family Family family	f.23.43.1 — ATP1G1/PLM/MAT8-like (FXYD-like)

CATH v4.4 (6 domains)

Domain ID domain_id	3a3yA01
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	3a3yA02
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	3a3yA03
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	3a3yA04
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	3a3yB01
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	3a3yB02
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	222.884 Å
Unit-cell length b length_b	50.720 Å
Unit-cell length c length_c	163.342 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2485
R_work r_work	0.2472
R_free r_free	0.2928

Crystal structure of the sodium-potassium pump with bound potassium and ouabain

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

Na, K-ATPase alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Phospholemman-like protein

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

3a3y__assembly_1__model_1

3a3y__assembly_1__model_1 | I(q)

3a3y__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 (10)

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 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the sodium-potassium pump with bound potassium and ouabain

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

Na, K-ATPase alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phospholemman-like protein

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

3a3y__assembly_1__model_1

3a3y__assembly_1__model_1 | I(q)

3a3y__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 (10)

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 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)