SMTL ID : 4ret.1 (1 other biounit)

Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 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.165, F.230 No protein-ligand interaction detected (PLIP)

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.2: 6 residues within 4Å: Chain A: K.982, P.983, T.984, W.985 Chain B: Y.68 Chain C: Y.21 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.984, A:K.982, A:T.984, A:T.984, A:W.985, B:Y.68 GLC-FRU.3: 6 residues within 4Å: Chain A: V.942, F.943, Q.944, G.946, M.947, K.948 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.942, A:M.947, A:K.948

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.374, T.376, D.715 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.376, A:T.376, A:D.715, A:D.715 MG.5: 2 residues within 4Å: Chain A: K.724, D.745 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.745, A:D.745 MG.6: 4 residues within 4Å: Chain A: S.780, N.781, E.784, D.809 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.784, A:D.809, H2O.1, H2O.1, H2O.1

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 9 residues within 4Å: Chain A: F.865, V.869, E.873, T.984, F.987, P.991 Chain B: T.53, V.56, T.60 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.53, B:V.56, A:F.865, A:F.865, A:V.869, A:T.984, A:P.991 Hydrogen bonds: A:E.873 CLR.13: 11 residues within 4Å: Chain A: W.929, T.960, Y.968, P.983, W.986, F.987, F.990 Chain C: V.26, G.29, G.30, F.33 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.929, A:T.960, A:Y.968, A:P.983, A:P.983, A:W.986, A:W.986, A:F.990, A:F.990, C:F.33, C:F.33 Hydrogen bonds: C:G.29, C:G.30

1 x DGX: DIGOXIN(Non-covalent)

DGX.8: 17 residues within 4Å: Chain A: Q.116, D.126, N.127, L.130, L.316, E.317, F.321, G.324, V.327, A.328, E.332, F.788, F.791, L.798, T.802, I.805, R.885 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.130, A:E.317, A:F.321, A:V.327, A:A.328, A:F.788, A:F.788, A:F.791, A:L.798 Hydrogen bonds: A:D.126

3 x 17F: O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine(Non-covalent)

17F.9: 7 residues within 4Å: Chain A: H.288, I.292, G.295, K.841, E.845 Chain B: R.27 Ligands: 17F.10 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.845, A:E.845, A:E.845, B:R.27 Salt bridges: A:H.288, B:R.27, B:R.27 17F.10: 6 residues within 4Å: Chain A: H.288, H.291, I.292, G.295 Chain B: I.16 Ligands: 17F.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.291 Salt bridges: A:H.291 17F.12: 10 residues within 4Å: Chain A: E.845, S.849, M.857, E.1018 Chain B: T.28, W.32, I.35, L.36, Y.39, Y.43 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.845, A:E.1018, B:T.28, B:T.28 Hydrophobic interactions: B:Y.39

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

NAG.11: 1 residues within 4Å: Chain B: N.265 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laursen, M. et al., Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-01-28

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: A
Sodium/potassium-transporting ATPase subunit beta-1: B
Na+/K+ ATPase gamma subunit transcript variant a: 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

Na+/K+ ATPase gamma subunit transcript variant a

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