SMTL ID : 8jbm.2 (1 other biounit)

Crystal structure of Na+,K+-ATPase in the E1.Mn2+ state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 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: 2 residues within 4Å: Chain B: N.158, E.228 No protein-ligand interaction detected (PLIP)

3 x MN: MANGANESE (II) ION(Non-covalent)

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

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 11 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, T.60 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.869, A:P.991, B:T.53, B:V.56, B:M.57 Hydrogen bonds: A:E.873 CLR.13: 10 residues within 4Å: Chain A: T.786, E.845, S.849, Y.852, G.853, M.857 Chain B: R.27, I.35, Y.39, Y.43 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.852, B:I.35, B:Y.39 Hydrogen bonds: B:R.27, B:R.27 CLR.15: 10 residues within 4Å: Chain A: W.929, Y.968, P.983, W.986, F.987 Chain C: V.26, G.29, G.30, F.33 Ligands: DMU.16 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.929, A:W.929, A:P.983, A:W.986, A:W.986, A:F.987, C:F.33, C:F.33

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

PCW.6: 7 residues within 4Å: Chain A: I.293, T.839, K.841, V.843, N.844, E.845, I.848 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.293 Hydrogen bonds: A:V.843 PCW.7: 8 residues within 4Å: Chain A: F.144, Y.147, Q.148, K.151, Y.822, K.950, F.954, E.958 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.144 Salt bridges: A:K.151 PCW.8: 5 residues within 4Å: Chain A: F.943, G.946, M.947, K.948 Ligands: PCW.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.947 Salt bridges: A:K.948 PCW.9: 3 residues within 4Å: Chain A: S.941, Q.944, R.1008 No protein-ligand interaction detected (PLIP) PCW.10: 5 residues within 4Å: Chain A: I.1006, R.1010, G.1013, W.1014 Chain B: F.38 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.1014 Salt bridges: A:R.1010, A:R.1010 Hydrophobic interactions: B:F.38 PCW.11: 7 residues within 4Å: Chain A: F.868, I.879 Chain B: F.50, I.51, I.54, Q.55, L.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.51 Hydrogen bonds: B:Q.55 PCW.12: 4 residues within 4Å: Chain A: M.947, K.948, I.953 Ligands: PCW.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.947, A:I.953

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

NAG.14: 3 residues within 4Å: Chain B: E.222, G.225, N.265 No protein-ligand interaction detected (PLIP)

1 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.16: 6 residues within 4Å: Chain C: Y.21, D.22, T.25, V.26, F.33 Ligands: CLR.15 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.33

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
C

B
D

C
E

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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