SMTL ID : 7e20.1

Cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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: 1 residues within 4Å: Chain B: N.158 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: T.779, S.782, N.783, E.786, D.811 Ligands: K.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.782, A:D.811 K.3: 8 residues within 4Å: Chain A: V.329, A.330, V.332, E.334, N.783, E.786, D.811 Ligands: K.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.332, A:E.786 K.4: 4 residues within 4Å: Chain A: L.725, K.726, A.728, D.747 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.747

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.376, T.378, D.717 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.376, A:T.378, A:D.717

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 10 residues within 4Å: Chain A: V.935, V.944, F.945, Q.947, G.948, M.949, F.992, S.995, F.999 Ligands: Y01.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.935, A:F.945, A:F.945, A:M.949, A:F.992, A:F.999, A:F.999 Hydrogen bonds: A:M.949 Y01.7: 11 residues within 4Å: Chain A: F.867, E.875, T.986, F.989, C.990, P.993 Chain B: I.49, T.53, V.56, T.60, T.67 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.49, B:T.53, B:V.56, A:F.867, A:P.993, A:P.993 Hydrogen bonds: B:T.60, B:T.67, A:E.875, A:E.875 Y01.8: 15 residues within 4Å: Chain A: T.788, I.792, M.859, A.862, L.863, F.866, F.870, P.880, I.881, L.884 Chain B: F.50, I.51, Q.55, L.58 Ligands: Y01.11 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.788, A:I.792, A:I.792, A:M.859, A:A.862, A:L.863, A:F.866, A:F.866, A:F.870, A:P.880, A:I.881, A:I.881, A:L.884, B:F.50, B:I.51 Hydrogen bonds: B:Q.55, B:Q.55 Y01.10: 9 residues within 4Å: Chain A: I.784, E.847, G.855, M.859 Chain B: L.25, G.26, R.27, W.32, Y.39 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.27, B:W.32, B:Y.39, A:I.784, A:E.847 Salt bridges: B:R.27 Y01.11: 5 residues within 4Å: Chain A: L.884 Chain B: Y.43, A.47, I.51 Ligands: Y01.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.43, B:A.47, B:I.51 Y01.13: 13 residues within 4Å: Chain A: W.931, T.962, Y.970, P.985, W.988, F.989, F.992 Chain C: T.25, V.26, G.29, G.30, F.33 Ligands: Y01.6 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:T.25, C:F.33, A:W.931, A:W.931, A:T.962, A:Y.970, A:P.985, A:W.988, A:F.989, A:F.992

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

PC1.9: 12 residues within 4Å: Chain A: L.997, V.1000, Y.1001, V.1004, R.1012, G.1015, W.1016 Chain B: K.34, L.37, F.38, I.41, F.42 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:K.34, B:L.37, B:F.38, B:F.38, B:F.38, B:I.41, B:I.41, B:F.42, A:L.997, A:Y.1001, A:Y.1001, A:V.1004, A:W.1016, A:W.1016 Salt bridges: B:K.34, A:R.1012 Hydrogen bonds: A:W.1016

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

NAG.12: 1 residues within 4Å: Chain B: N.265 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Cryo-EM structures of recombinant human sodium-potassium pump determined in three different states. Nat Commun (2022)

Release Date

2022-06-15

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: A
Sodium/potassium-transporting ATPase subunit beta-1: B
Sodium/potassium-transporting ATPase subunit gamma: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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

Sodium/potassium-transporting ATPase subunit gamma

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