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

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC.1: 7 residues within 4Å: Chain A: H.107, D.111, N.114, S.116, R.154, L.163, T.166 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.163

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN.2: 3 residues within 4Å: Chain A: N.159, E.230, Q.264 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-FUC.3: 3 residues within 4Å: Chain A: N.194, T.196, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.196

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.4: 1 residues within 4Å: Chain A: N.267 No protein-ligand interaction detected (PLIP)

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 4 residues within 4Å: Chain A: G.49, I.52, G.53, Q.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.52, A:Q.56 CLR.6: 6 residues within 4Å: Chain A: R.28, Y.40, Y.44 Chain B: E.852, S.856 Ligands: PCW.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.40 Hydrogen bonds: A:R.28, A:R.28 CLR.18: 11 residues within 4Å: Chain B: W.936, Y.975, P.990, W.993, F.997 Chain C: L.39, V.42, G.43, V.46 Ligands: PCW.10, PCW.14 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.936, B:P.990, B:W.993, B:W.993, B:F.997, C:V.46

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

PCW.7: 3 residues within 4Å: Chain B: K.158, Y.829, I.958 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.158 PCW.8: 2 residues within 4Å: Chain B: H.295, H.298 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.295 PCW.9: 15 residues within 4Å: Chain A: K.35, F.39, F.43, L.47, I.50 Chain B: I.865, Y.999, I.1002, L.1005, Y.1006, M.1009, I.1013, W.1021, V.1022, Q.1024 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.865, B:Y.999, B:I.1002, B:I.1002, B:L.1005, B:Y.1006, B:Y.1006, B:I.1013, B:V.1022, A:F.43, A:L.47, A:I.50, A:I.50 Hydrogen bonds: B:W.1021 Salt bridges: A:K.35 PCW.10: 18 residues within 4Å: Chain B: W.936, I.949, F.950, Q.951, Q.952, G.953, M.954, K.955, L.963, F.964, T.967, F.997, S.1000, L.1001 Chain C: L.50 Ligands: PCW.11, PCW.14, CLR.18 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.936, B:I.949, B:F.950, B:L.963, B:F.964, B:F.964, B:F.997, B:L.1001, C:L.50 Hydrogen bonds: B:M.954 Salt bridges: B:K.955 PCW.11: 8 residues within 4Å: Chain B: Q.951, F.1004, L.1005, E.1008, F.1012, R.1015, R.1016 Ligands: PCW.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.1005, B:E.1008 Hydrogen bonds: B:Q.951, B:Q.951 Salt bridges: B:R.1015 PCW.12: 9 residues within 4Å: Chain B: Y.136, T.143, G.818, L.969, F.972, C.976, P.977, A.982 Ligands: PCW.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.972, B:A.982 PCW.13: 15 residues within 4Å: Chain A: Y.44, A.48, F.51, I.52, I.55, L.59 Chain B: T.793, M.864, L.868, F.871, F.875, P.885, M.886, I.889 Ligands: CLR.6 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.793, B:L.868, B:F.871, B:F.875, B:I.889, A:Y.44, A:Y.44, A:A.48, A:I.52 Hydrogen bonds: A:Q.56 PCW.14: 7 residues within 4Å: Chain B: F.964, P.990 Chain C: Y.34, V.42, L.50 Ligands: PCW.10, CLR.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.42, B:F.964 PCW.15: 12 residues within 4Å: Chain A: F.16, G.27 Chain B: F.296, I.300, V.303, N.336, I.792, K.848, V.850, N.851, E.852, Y.859 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.300, B:V.303, B:I.792, B:V.850, B:Y.859 Hydrogen bonds: B:E.852 Salt bridges: B:K.848, B:E.852 PCW.19: 8 residues within 4Å: Chain B: C.976, P.977 Chain C: Y.36, R.40, V.41, L.44, I.45 Ligands: PCW.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.44, C:I.45 Salt bridges: C:R.40

2 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 4 residues within 4Å: Chain B: T.784, S.787, E.791, D.816 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.787, B:E.791, B:D.816, H2O.1, H2O.1 MG.17: 2 residues within 4Å: Chain B: K.731, D.752 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.752, H2O.1

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

Na+,K+-ATPase beta subunit: A
Na, K-ATPase alpha subunit: B
FXYD domain-containing ion transport regulator: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
E

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Na+,K+-ATPase beta subunit

Na, K-ATPase alpha subunit

FXYD domain-containing ion transport regulator

Related Entries With Identical Sequence