SMTL ID : 6kpu.1 (1 other biounit)

Crystal structures of Na+,K+-ATPase in complex with beryllium fluoride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.62 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

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

MG.3: 6 residues within 4Å: Chain A: D.374, T.376, D.715, G.716, D.719 Ligands: BEF.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.374, A:T.376, A:D.715, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain A: E.332, N.781, E.784, D.809 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.332, A:E.784, A:D.809, H2O.1, H2O.1

1 x NA: SODIUM ION

NA.4: 4 residues within 4Å: Chain A: G.277, K.724, A.726, D.745 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.745

1 x BEF: BERYLLIUM TRIFLUORIDE ION

BEF.6: 9 residues within 4Å: Chain A: G.218, D.374, K.375, T.376, T.615, G.616, K.696, N.718 Ligands: MG.3 No protein-ligand interaction detected (PLIP)

1 x 1AT: beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside

1AT.7: 7 residues within 4Å: Chain A: V.942, F.943, G.946, M.947, K.948, L.994, F.997 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.942, A:L.994, A:F.997 Hydrogen bonds: A:M.947

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.8: 3 residues within 4Å: Chain B: N.193, K.203, N.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.205

1 x CLR: CHOLESTEROL

CLR.9: 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 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.929, A:W.929, A:W.929, A:T.960, A:W.986, A:W.986, A:W.986, A:W.986, A:W.986, A:F.987, A:F.987, A:F.990, A:F.990, A:F.990, C:F.33, C:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogawa, H. et al., X-ray crystal structures of Na+,K+-ATPase in complex with cardiotonic steroids. To Be Published

Release Date

2020-09-02

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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