SMTL ID : 9vj2.1

Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.79 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: 5 residues within 4Å: Chain B: N.158, D.171, K.173, E.228, F.230 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.374, T.376, D.715, G.716, D.719 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.376, A:D.715, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain A: L.723, K.724, A.726, D.745 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.745, H2O.1

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 11 residues within 4Å: Chain A: W.929, T.960, Y.968, P.983, W.986, F.987, F.990 Chain C: V.26, G.29, G.30, F.33 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.929, A:W.929, A:T.960, A:Y.968, A:W.986, A:W.986, A:W.986, A:F.990, C:F.33, C:F.33, C:F.33 Hydrogen bonds: C:G.29 CLR.5: 7 residues within 4Å: Chain A: E.873, T.984, F.987, C.988, P.991 Chain B: V.56, T.60 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.991 Hydrogen bonds: A:T.984

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

PCW.6: 4 residues within 4Å: Chain A: F.868, I.879 Chain B: Q.55, L.58 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.868 Hydrogen bonds: B:Q.55 PCW.7: 4 residues within 4Å: Chain A: Y.147, Q.148, K.151, K.347 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.147 Hydrogen bonds: A:Q.148 Salt bridges: A:K.151, A:K.151, A:K.347 PCW.8: 3 residues within 4Å: Chain A: I.292, E.845 Chain B: I.16 No protein-ligand interaction detected (PLIP) PCW.9: 5 residues within 4Å: Chain A: R.351, Y.822, I.951, F.954 Chain C: I.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.351 PCW.10: 3 residues within 4Å: Chain A: L.1005, I.1006, R.1009 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1009 PCW.11: 2 residues within 4Å: Chain A: M.947, K.948 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.948

1 x 01: palytoxin

01.12: 26 residues within 4Å: Chain A: A.112, Q.116, T.119, E.120, Q.124, D.126, N.127, L.130, L.309, I.310, E.312, Y.313, T.314, W.315, L.316, E.317, I.320, V.327, A.328, V.330, E.332, N.781, E.784, F.788, T.802, I.805 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Q.116, A:T.119, A:L.130, A:E.312, A:T.314, A:W.315, A:L.316, A:I.320, A:A.328, A:E.332, A:F.788 Hydrogen bonds: A:I.115, A:Q.116, A:E.120, A:Q.124, A:D.126, A:D.126, A:L.309, A:I.310, A:E.317, A:E.317, A:A.328

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

NAG.13: 3 residues within 4Å: Chain B: E.222, T.226, N.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.226, B:N.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., How palytoxin transforms the Na + ,K + pump into a cation channel. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-10-01

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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