SMTL ID : 7d93.1 (1 other biounit)

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 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) NAG-NAG.2: 2 residues within 4Å: Chain B: T.226, N.265 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.369, T.371, D.710, G.711 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.371, A:D.710, A:D.710, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain A: E.327, E.779, D.804 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.327, A:E.779, A:D.804, H2O.1, H2O.1

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

NA.4: 4 residues within 4Å: Chain A: G.272, K.719, A.721, D.740 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.721

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: V.864, E.868, T.979, F.982, C.983, P.986 Chain B: V.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.986 Hydrogen bonds: A:T.979 CLR.13: 3 residues within 4Å: Chain A: F.938, L.989, V.993 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.938, A:L.989, A:V.993 CLR.15: 11 residues within 4Å: Chain A: W.924, T.955, Y.963, P.978, W.981, F.982, F.985 Chain C: V.26, G.29, G.30, F.33 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.924, A:T.955, A:Y.963, A:P.978, A:W.981, A:W.981, A:F.982, A:F.982, A:F.985, C:F.33, C:F.33

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

PCW.7: 6 residues within 4Å: Chain A: F.139, Y.142, Q.143, K.146, K.342 Ligands: PCW.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.143 Salt bridges: A:K.146, A:K.342 PCW.8: 6 residues within 4Å: Chain A: H.283, K.833, K.836, N.839, E.840 Chain B: L.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.840 PCW.9: 4 residues within 4Å: Chain A: L.339, V.810, Y.817 Ligands: PCW.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.810 Hydrogen bonds: A:Y.817, A:Y.817 PCW.10: 2 residues within 4Å: Chain A: R.1005, W.1009 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.1008, A:W.1009 Salt bridges: A:R.1005 PCW.11: 5 residues within 4Å: Chain A: V.937, F.938, G.941, M.942, K.943 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.943

1 x H0C: [(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S},5~{S},8~{R},9~{S},10~{R},11~{R},13~{R},14~{S},17~{R})-10-(hydroxymethyl)-13-methyl-1,5,11,14-tetrakis(oxidanyl)-17-(5-oxidanylidene-2~{H}-furan-3-yl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-6-methyl-3,5-bis(oxidanyl)oxan-4-yl] anthracene-9-carboxylate(Non-covalent)

H0C.12: 18 residues within 4Å: Chain A: Q.111, E.115, E.117, Q.119, N.122, L.125, Y.308, E.312, I.315, F.316, G.319, V.322, A.323, F.783, L.793, T.797, R.880, D.884 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.115, A:L.125, A:Y.308, A:F.316, A:F.783, A:F.783, A:L.793 Hydrogen bonds: A:Q.111, A:E.115, A:Q.119, A:Q.119, A:N.122, A:R.880 Salt bridges: A:R.880

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

NAG.14: 3 residues within 4Å: Chain B: N.193, K.203, N.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.203, B:N.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-01-27

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: 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-1

Sodium/potassium-transporting ATPase subunit beta-1

FXYD domain-containing ion transport regulator

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