SMTL ID : 7d92.1

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P4(3)2(1)2 symmetry)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.90 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: 1 residues within 4Å: Chain B: N.158 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.369, T.371, D.710, G.711, D.714 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.3: 4 residues within 4Å: Chain A: S.718, K.719, A.721, D.740 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.740, H2O.1 MG.4: 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

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 7 residues within 4Å: Chain A: F.860, E.868, T.979, F.982, C.983, P.986 Chain B: V.56 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.860, A:P.986, B:V.56 Hydrogen bonds: A:T.979 CLR.15: 7 residues within 4Å: Chain A: S.844, M.852 Chain B: R.27, I.35, Y.39, Y.43 Ligands: PCW.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.35, B:Y.39, B:Y.39 Hydrogen bonds: B:R.27 CLR.17: 10 residues within 4Å: Chain A: W.924, T.955, Y.963, P.978, W.981, F.982, F.985 Chain C: V.26, G.30, F.33 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:F.33, C:F.33, C:F.33, C:F.33, A:W.924, A:T.955, A:W.981, A:F.982, A:F.985 Hydrogen bonds: C:V.26

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

PCW.6: 5 residues within 4Å: Chain A: F.863, I.874 Chain B: F.50, Q.55, L.58 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.50, A:F.863 Hydrogen bonds: B:Q.55 PCW.7: 5 residues within 4Å: Chain A: F.139, Y.142, Q.143, K.146, K.342 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.139, A:Y.142 Hydrogen bonds: A:Q.143 Salt bridges: A:K.146, A:K.342 PCW.8: 4 residues within 4Å: Chain A: G.290, V.291, E.840 Ligands: CLR.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.840 PCW.9: 3 residues within 4Å: Chain A: L.339, R.346, Y.817 No protein-ligand interaction detected (PLIP) PCW.10: 5 residues within 4Å: Chain A: I.1001, R.1004, R.1005 Ligands: PCW.12, PCW.13 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.1004, A:R.1005 PCW.11: 3 residues within 4Å: Chain A: G.941, M.942, K.943 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.942 Salt bridges: A:K.943 PCW.12: 2 residues within 4Å: Chain A: R.1004 Ligands: PCW.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1004 PCW.13: 5 residues within 4Å: Chain A: R.1005, W.1009, V.1010 Chain B: K.34 Ligands: PCW.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.1010 Salt bridges: A:R.1005, A:R.1005

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.14: 18 residues within 4Å: Chain A: Q.111, T.114, E.115, Q.119, N.122, L.125, Y.308, E.312, I.315, F.316, G.319, V.322, A.323, F.783, F.786, T.797, R.880, D.884 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.115, A:Y.308, A:F.316, A:A.323, A:F.783, A:F.783, A:F.783 Hydrogen bonds: A:Q.111, A:Q.119, A:Q.119, A:I.315, A:R.880, A:D.884, A:D.884

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

NAG.16: 4 residues within 4Å: Chain B: E.222, G.225, T.226, 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

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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