SMTL ID : 8jbl.1 (1 other biounit)

Crystal structure of Na+,K+-ATPase in the E1.Mg2+ state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 3 residues within 4Å: Chain B: N.158, D.171, K.173 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 1 residues within 4Å: Chain B: N.265 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.374, D.715, D.719 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.715, H2O.1 MG.4: 3 residues within 4Å: Chain A: S.780, E.784, D.809 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.780, A:E.784, A:D.809, H2O.1 MG.5: 5 residues within 4Å: Chain A: L.723, K.724, A.726, D.727, D.745 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.726, A:D.745, H2O.1

3 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 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.53, B:V.56, B:M.57, A:V.869, A:P.991 Hydrogen bonds: A:E.873, A:T.984 CLR.7: 11 residues within 4Å: Chain A: W.929, Y.968, P.983, W.986, F.987, F.990 Chain C: V.26, G.29, G.30, F.33 Ligands: PC1.13 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.33, C:F.33, C:F.33, A:W.929, A:W.929, A:P.983, A:P.983, A:W.986, A:W.986, A:F.987, A:F.987, A:F.990 Hydrogen bonds: C:T.25, C:G.30 CLR.12: 7 residues within 4Å: Chain A: E.845, S.849 Chain B: R.27, I.35, Y.39, Y.43 Ligands: PC1.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.35, B:Y.39, B:Y.39, B:Y.43

3 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.8: 15 residues within 4Å: Chain A: I.292, I.293, V.296, L.300, N.329, I.785, L.789, I.793, V.843, N.844, E.845, Y.852 Chain B: F.15 Ligands: PCW.11, CLR.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.292, A:I.293, A:V.296, A:L.300, A:I.785, A:L.789, A:I.793, A:Y.852 Hydrogen bonds: A:E.845 Salt bridges: A:E.845 PC1.10: 12 residues within 4Å: Chain A: S.941, F.943, Q.944, L.994, F.997, V.998, E.1001, V.1002, L.1005, R.1008 Ligands: PC1.13, PCW.14 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.943, A:F.943, A:F.943, A:F.943, A:L.994, A:F.997, A:V.998, A:E.1001, A:V.1002 PC1.13: 11 residues within 4Å: Chain A: V.933, F.943, Q.944, G.946, M.947, L.956, F.957, F.997 Chain C: F.33 Ligands: CLR.7, PC1.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.956, A:F.957, C:F.33, C:F.33

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

PCW.9: 7 residues within 4Å: Chain A: Y.147, Q.148, K.151, I.951, F.954, E.958 Chain C: I.45 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.954, A:E.958 Hydrogen bonds: A:Y.147, A:Q.148 Salt bridges: A:K.151 PCW.11: 3 residues within 4Å: Chain A: I.292, V.296 Ligands: PC1.8 No protein-ligand interaction detected (PLIP) PCW.14: 4 residues within 4Å: Chain A: Q.944, R.1008, R.1009 Ligands: PC1.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.1009 Salt bridges: A:R.1008 PCW.15: 4 residues within 4Å: Chain A: I.1006, R.1010, W.1014, V.1015 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1010 PCW.16: 4 residues within 4Å: Chain A: E.873, T.984 Chain B: Y.68 Chain C: Y.21 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:Y.21, B:Y.68 Salt bridges: A:E.873 PCW.17: 2 residues within 4Å: Chain A: V.1002, R.1009 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1002 PCW.18: 13 residues within 4Å: Chain A: A.136, I.140, C.807, G.811, F.965, C.969, P.970, G.971, M.972, V.974, A.975, L.976 Chain C: R.27 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:R.27, A:G.971 Hydrophobic interactions: A:A.136, A:I.140, A:F.965, A:F.965

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., Crystal structures of Na + ,K + -ATPase reveal the mechanism that converts the K + -bound form to Na + -bound form and opens and closes the cytoplasmic gate. Febs Lett. (2023)

Release Date

2023-08-09

Peptides

Sodium/potassium-transporting ATPase subunit alpha: 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

Sodium/potassium-transporting ATPase subunit beta-1

FXYD domain-containing ion transport regulator

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