SMTL ID : 7ddh.1 (1 other biounit)

Crystal structures of Na+,K+-ATPase in complex with digoxin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.46 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain B: N.158, E.228, F.230 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: T.226, N.265 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.369, T.371, D.710, G.711, D.714 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.371, A:D.710, A:D.710, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain A: E.327, E.779, D.804 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.327, A:E.779, A:D.804, H2O.1, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: G.272, K.719, D.740 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.740

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: F.860, V.864, E.868, T.979, C.983, P.986 Chain B: V.56 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.860, A:P.986 Hydrogen bonds: A:T.979 CLR.14: 7 residues within 4Å: Chain A: F.299, E.840 Chain B: R.27, I.35, Y.39, Y.43 Ligands: PCW.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.35, B:Y.39, B:Y.43, A:F.299 Hydrogen bonds: B:R.27 CLR.16: 11 residues within 4Å: Chain A: W.924, T.955, Y.963, P.978, W.981, F.982, F.985 Chain C: V.26, G.29, G.30, F.33 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.924, A:T.955, A:Y.963, A:P.978, A:W.981, A:F.982, A:F.985, C:F.33, C:F.33

6 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.7: 7 residues within 4Å: Chain A: C.138, F.139, Y.142, Q.143, K.146, K.342 Ligands: PCW.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.142, A:Q.143, A:Q.143 Salt bridges: A:K.146, A:K.342 PCW.8: 10 residues within 4Å: Chain A: H.283, I.287, G.290, T.834, K.836, N.839, E.840 Chain B: L.25 Ligands: CLR.14, PCW.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.840 PCW.9: 1 residues within 4Å: Chain A: Y.817 No protein-ligand interaction detected (PLIP) PCW.10: 3 residues within 4Å: Chain A: E.81, K.149 Ligands: PCW.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.149 PCW.11: 5 residues within 4Å: Chain A: V.937, F.938, G.941, M.942, K.943 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.943 PCW.15: 4 residues within 4Å: Chain A: H.283, H.286 Chain B: K.13 Ligands: PCW.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.283, A:H.286, B:K.13, B:K.13

1 x DGX: DIGOXIN(Non-covalent)

DGX.12: 15 residues within 4Å: Chain A: Q.111, E.115, Q.119, N.122, L.125, E.312, F.316, G.319, V.322, A.323, F.783, T.797, I.800, R.880 Chain B: Q.84 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.312, A:F.316, A:A.323, A:F.783, A:F.783 Hydrogen bonds: A:Q.119, A:N.122, A:T.797, A:R.880

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 3 residues within 4Å: Chain B: N.193, K.203, N.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.203, B:N.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-01-27

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: A
Sodium/potassium-transporting ATPase subunit beta-1: B
FXYD domain-containing ion transport regulator: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

Membrane

We predict this structure to be a membrane protein.
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Sodium/potassium-transporting ATPase subunit alpha-1

Sodium/potassium-transporting ATPase subunit beta-1

FXYD domain-containing ion transport regulator

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