SMTL ID : 7e21.1

Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S

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

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: A.330, N.331, S.782, N.783, E.786, D.811 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.330, A:D.811 NA.3: 3 residues within 4Å: Chain A: V.329, V.332, D.811 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.329 Water bridges: A:G.335 NA.4: 5 residues within 4Å: Chain A: Y.778, T.781, S.782, Q.930, D.933 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.778, A:T.781, A:S.782, A:Q.930, A:D.933 NA.5: 3 residues within 4Å: Chain A: L.725, A.728, D.747 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.747

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 1 residues within 4Å: Ligands: AGS.7 No protein-ligand interaction detected (PLIP)

1 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.7: 16 residues within 4Å: Chain A: D.376, K.377, T.378, D.450, S.452, F.482, S.484, K.487, K.508, G.509, R.551, L.553, G.618, D.619, R.692 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.377, A:T.378, A:T.378, A:D.450, A:S.452, A:K.508, A:R.551, A:G.618, A:G.618, A:D.619, A:R.692 Salt bridges: A:R.551 pi-Stacking: A:F.482, A:F.482

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 10 residues within 4Å: Chain A: V.935, V.944, F.945, Q.947, G.948, M.949, K.950, S.995, L.996, F.999 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.935, A:V.944, A:F.945, A:L.996, A:F.999 Salt bridges: A:K.950, A:K.950 Y01.9: 8 residues within 4Å: Chain A: V.871, E.875, T.986, F.989, C.990, P.993 Chain B: T.53, V.56 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.871, A:T.986, A:P.993, B:T.53, B:V.56 Y01.10: 14 residues within 4Å: Chain A: I.792, A.862, L.863, F.866, F.870, P.880, I.881 Chain B: F.50, I.51, I.54, Q.55, L.58 Ligands: Y01.11, Y01.13 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.792, A:I.792, A:A.862, A:F.866, A:F.866, A:F.870, A:F.870, A:P.880, A:I.881, B:F.50, B:I.51, B:L.58 Y01.11: 8 residues within 4Å: Chain A: I.792, I.795, A.796, L.884, G.885 Ligands: Y01.10, PC1.12, Y01.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.795, A:A.796 Y01.13: 6 residues within 4Å: Chain A: I.881 Chain B: Y.43, A.47, I.51 Ligands: Y01.10, Y01.11 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.881, B:A.47, B:I.51, B:I.51 Y01.16: 9 residues within 4Å: Chain A: W.931, T.962, Y.970, P.985, W.988 Chain C: V.26, G.29, G.30, F.33 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.931, A:W.931, A:W.931, A:T.962, A:P.985, A:W.988, A:W.988, C:V.26, C:F.33, C:F.33, C:F.33

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

PC1.12: 13 residues within 4Å: Chain A: I.294, I.295, L.302, I.784, T.788, L.791, V.845, N.846, E.847, I.850, M.859 Chain B: F.15 Ligands: Y01.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.294, A:I.295, A:L.302, A:I.784, A:T.788, A:L.791, A:I.850 Salt bridges: A:E.847 PC1.14: 10 residues within 4Å: Chain A: L.997, V.1000, Y.1001, V.1004, W.1016 Chain B: K.34, L.37, F.38, I.41, L.46 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.1000, A:Y.1001, A:Y.1001, A:V.1004, A:W.1016, B:L.37, B:F.38, B:F.38, B:I.41, B:L.46 Salt bridges: A:R.1012, B:K.34, B:K.34

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

NAG.15: 3 residues within 4Å: Chain B: G.225, N.265, T.267 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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