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

Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 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: 4 residues within 4Å: Chain B: N.158, E.165, E.228, F.230 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.3: 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.4: 3 residues within 4Å: Chain A: 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

1 x OBN: OUABAIN(Non-covalent)

OBN.5: 17 residues within 4Å: Chain A: Q.116, E.122, P.123, D.126, N.127, L.130, E.317, I.320, G.324, V.327, A.328, F.788, F.791, L.798, T.802, I.805, R.885 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.130, A:I.320, A:A.328, A:F.788, A:F.788, A:F.791, A:L.798 Hydrogen bonds: A:Q.116, A:D.126, A:D.126, A:E.317

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 10 residues within 4Å: Chain A: F.865, V.869, E.873, T.984, F.987, C.988, P.991 Chain B: T.53, V.56, M.57 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.53, B:V.56, B:M.57, A:F.865, A:P.991 Hydrogen bonds: A:T.984 CLR.15: 12 residues within 4Å: Chain A: W.929, T.960, Y.968, P.983, W.986, F.987 Chain C: V.26, G.29, G.30, F.33 Ligands: 1DS.8, 17F.16 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:W.929, A:T.960, A:Y.968, A:P.983, A:W.986, A:W.986, A:W.986, C:F.33, C:F.33, C:F.33 Hydrogen bonds: C:T.25, C:G.30

1 x 1AT: beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside(Non-covalent)

1AT.7: 5 residues within 4Å: Chain A: V.942, F.943, G.946, M.947, K.948 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.942, A:F.943 Hydrogen bonds: A:M.947, A:M.947, A:K.948, A:K.948

1 x 1DS: 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside(Non-covalent)

1DS.8: 8 residues within 4Å: Chain A: K.982, P.983, T.984, F.987 Chain B: Y.68 Chain C: Y.21 Ligands: CLR.15, 17F.16 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.987 Hydrogen bonds: A:T.984, C:Y.21, C:Y.21, B:Y.68

4 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, E.845, I.848, S.849 Ligands: 17F.10, 17F.14 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.292, A:I.848 Hydrogen bonds: A:E.845 Salt bridges: A:H.288, B:R.27 17F.10: 7 residues within 4Å: Chain A: H.288, H.291, I.292, G.295, V.296 Chain B: I.16 Ligands: 17F.9 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.288, A:H.291 17F.14: 10 residues within 4Å: Chain A: E.845, S.849, E.1018 Chain B: T.28, S.31, W.32, I.35, Y.39, Y.43 Ligands: 17F.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.1018 Hydrophobic interactions: B:I.35 17F.16: 8 residues within 4Å: Chain A: F.957 Chain C: I.32, F.33, L.36, A.37, V.40 Ligands: 1DS.8, CLR.15 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.33, C:L.36, C:V.40, A:F.957

1 x CE1: O-DODECANYL OCTAETHYLENE GLYCOL(Non-covalent)

CE1.11: 10 residues within 4Å: Chain A: R.1010, G.1013, W.1014, V.1015 Chain B: K.34, L.37, F.38, I.41, F.42, C.45 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.37, B:F.38, B:I.41, B:F.42 Hydrogen bonds: B:K.34, A:R.1010, A:R.1010, A:W.1014, A:V.1015

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

NAG.12: 3 residues within 4Å: Chain B: N.193, K.203, N.205 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.193 Hydrogen bonds: B:N.205 NAG.13: 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., Crystal structure of the high-affinity Na+,K+-ATPase-ouabain complex with Mg2+ bound in the cation binding site. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-06-26

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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