3KDP: Sodium-potassium pump

Crystal structure of the sodium-potassium pump. Determined by X-ray diffraction at 3.5 Å resolution. Released 16 Feb 2010.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Sus scrofa
Chains: 6
Atoms: 20,630
Mol. weight: 294.29 kDa
Ligands: MF4, CLR, RB, MG
Released: 16 Feb 2010

Explore 3KDP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KDP contains 131 α-helices and 104 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 59 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	28-30	3
α-helix	41-46	6
β-strand	56	1	1
α-helix	62-68	7
α-helix	75-77	3
α-helix	86-88	3
α-helix	93-111	19
α-helix	121-139	19
α-helix	151-154	4
β-strand	161-167	7	1
β-strand	169-174	6	1
α-helix	175-177	3
β-strand	183-184	2	1
β-strand	191	1	1
β-strand	195-207	13	1
α-helix	209-212	4
β-strand	218-220	3	1
β-strand	235-236	2	1
β-strand	241-253	13	1
α-helix	255-257	3
α-helix	261-267	7
α-helix	278-301	24
α-helix	314-322	9
α-helix	330-344	15
β-strand	349-351	3	2
α-helix	356-359	4
α-helix	360-362	3
β-strand	365-368	4	2
α-helix	370-374	5
β-strand	375	1	3
β-strand	380-384	5	4
α-helix	386-388	3
α-helix	390	1
β-strand	391-392	2	4
α-helix	409-420	12
β-strand	426	1	5
α-helix	427	1
α-helix	435-437	3
β-strand	440	1	5
α-helix	444-456	13
β-strand	468-473	6	4
β-strand	481-487	7	4
β-strand	497-502	6	4
α-helix	505-507	3
β-strand	511-513	3	4
β-strand	516	1	6
β-strand	519	1	6
β-strand	522	1	4
α-helix	525-539	15
β-strand	544-552	9	4
β-strand	576-585	10	4
α-helix	587	1
β-strand	588	1	3
α-helix	589	1
α-helix	591-601	11
α-helix	604	1
β-strand	605-610	6	2
α-helix	614-624	11
α-helix	634-638	5
α-helix	645-647	3
α-helix	650-652	3
β-strand	655-659	5	2
α-helix	660-663	4
α-helix	668-676	9
β-strand	680-684	5	2
α-helix	688-700	13
β-strand	705-708	4	2
α-helix	715-718	4
β-strand	723-727	5	2
α-helix	733-737	5
β-strand	741-743	3	2
α-helix	750-774	25
α-helix	777-788	12
α-helix	797-800	4
α-helix	803-807	5
α-helix	809-813	5
α-helix	815-817	3
α-helix	824-826	3
α-helix	828-830	3
α-helix	840-846	7
α-helix	850-867	18
α-helix	873-876	4
α-helix	880-883	4
β-strand	891-892	2	7
β-strand	898-899	2	7
α-helix	901-927	27
α-helix	937-940	4
α-helix	947-963	17
α-helix	967-971	5
α-helix	978-980	3
α-helix	985-1004	20
α-helix	1009-1014	6

Chains B and D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	33-55	23
α-helix	56-58	3
β-strand	79	1	8
β-strand	87-89	3	9
α-helix	99-109	11
β-strand	123-124	2	10
β-strand	148-149	2	10
α-helix	153-155	3
β-strand	176	1	11
β-strand	178	1	8
β-strand	184	1	12
β-strand	208	1	13
β-strand	211-214	4	14
β-strand	227	1	15
β-strand	239	1	13
α-helix	243	1
β-strand	245	1	12
β-strand	261	1	11
β-strand	263	1	15
β-strand	274	1	16
β-strand	275-278	4	14
β-strand	297	1	16
β-strand	298-300	3	9

Chain C: 60 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	28-30	3
α-helix	41-46	6
β-strand	56	1	1
α-helix	62-68	7
α-helix	75-77	3
α-helix	81-87	7
α-helix	88-90	3
α-helix	94-113	20
α-helix	121-141	21
α-helix	142-144	3
α-helix	151-154	4
β-strand	161-167	7	1
β-strand	169-174	6	1
α-helix	175-177	3
β-strand	183-184	2	1
β-strand	191	1	1
β-strand	195-207	13	1
α-helix	209-212	4
β-strand	218-220	3	1
β-strand	235-236	2	1
β-strand	241-253	13	1
α-helix	255-257	3
α-helix	261-267	7
α-helix	278-298	21
α-helix	302-305	4
α-helix	310-320	11
α-helix	327-344	18
β-strand	349-351	3	17
α-helix	356-359	4
α-helix	360-362	3
β-strand	365-368	4	17
α-helix	370-374	5
β-strand	375	1	18
β-strand	380-384	5	19
α-helix	386-388	3
α-helix	390	1
β-strand	391-392	2	19
α-helix	409-420	12
β-strand	426	1	20
α-helix	435-437	3
β-strand	440	1	20
α-helix	444-456	13
β-strand	468-473	6	19
β-strand	481-487	7	19
β-strand	497-502	6	19
α-helix	505-507	3
β-strand	511-513	3	19
β-strand	516	1	21
β-strand	519	1	21
β-strand	522	1	19
α-helix	525-539	15
β-strand	544-552	9	19
β-strand	576-585	10	19
α-helix	587	1
β-strand	588	1	18
α-helix	589	1
α-helix	591-601	11
β-strand	605-609	5	17
α-helix	614-624	11
α-helix	634-638	5
α-helix	645-647	3
α-helix	650-652	3
β-strand	655-659	5	17
α-helix	660-663	4
α-helix	668-676	9
β-strand	680-684	5	17
α-helix	688-700	13
β-strand	705-708	4	17
α-helix	715-718	4
β-strand	723-727	5	17
α-helix	733-737	5
β-strand	741-743	3	17
α-helix	750-774	25
α-helix	777-788	12
α-helix	797-800	4
α-helix	803-807	5
α-helix	809-813	5
α-helix	815-817	3
α-helix	824-826	3
α-helix	828-830	3
α-helix	840-846	7
α-helix	850-867	18
α-helix	873-876	4
α-helix	880-883	4
β-strand	891-892	2	22
β-strand	898-899	2	22
α-helix	902-927	26
α-helix	937-940	4
α-helix	947-963	17
α-helix	967-971	5
α-helix	978-980	3
α-helix	985-1004	20
α-helix	1009-1014	6

Chains G and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	24-45	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/potassium-transporting ATPase subunit alpha-1	A, C	protein	998	Sus scrofa	P05024 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-1	B, D	protein	286	Sus scrofa	P05027 (AlphaFold model)
Na+/K+ ATPase gamma subunit transcript variant a	G, H	protein	27	Sus scrofa	Q58K79 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3KDP_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A, C)
AKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPT
TPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGC
FSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRI
ISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRT
VMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLI
GIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNR
MTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKR
AVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLL
VMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQF
PEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAK
AIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYH
TEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKKADIGVAMGIAGSDVSKQA
ADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTV
TILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNEQLISMAYGQIGMIQALGG
FFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTPFFVT
IVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKP
TWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Sequence of entity 2 (B, D), FASTA

>3KDP_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
NSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVAPPGL
TQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDDMIFEDCGNVPSELKERG
EYNNERGERKVCRSRLEWLGNCSGLNDETYGYKDGKPCVIIKLNRVLGFKPKPPKNESLE
TYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPLQYYPYYGKLLQPKYLQP
LMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS

Sequence of entity 3 (G, H), FASTA

>3KDP_3 Na+/K+ ATPase gamma subunit transcript variant a (chains G, H)
YETVRNGGLIFAALAFIVGLIILLSKR

Ligands and cofactors

ID	Name	Formula	Copies
MF4	TETRAFLUOROMAGNESATE(2-)	F4 Mg	2
CLR	Cholesterol	C27 H46 O	2
RB	Rubidium ion	Rb	6
MG	Magnesium ion	Mg	2

Primary citation

Crystal structure of the sodium-potassium pump. Morth, J.P., Pedersen, B.P., Toustrup-Jensen, M.S. et al. Nature (2007) 450:1043-1049. DOI 10.1038/nature06419 · PubMed

Other PDB entries of the same protein (UniProt P05024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WGU 2.8 Å, Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state without oligomycin
3WGV 2.8 Å, Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin
8JBK 2.8 Å, Crystal structure of Na+,K+-ATPase in the E1.3Na+ state
7WYT 2.9 Å, Crystal structures of Na+,K+-ATPase in complex with ouabain
8JBM 2.9 Å, Crystal structure of Na+,K+-ATPase in the E1.Mn2+ state
8JBL 3.0 Å, Crystal structure of Na+,K+-ATPase in the E1.Mg2+ state
7DDL 3.2 Å, Crystal structures of Na+,K+-ATPase in complex with bufalin
7D91 3.35 Å, Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ (P4(3)2(1)2…
4HYT 3.4 Å, Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site
4RES 3.41 Å, Crystal structure of the Na,K-ATPase E2P-bufalin complex with bound potassium
7DDH 3.46 Å, Crystal structures of Na+,K+-ATPase in complex with digoxin
3B8E 3.5 Å, Crystal structure of the sodium-potassium pump

Browse structure collections

About this viewer

MolViewer shows 3KDP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.