SMTL ID : 7qtv.1

Beryllium fluoride form of the Na+,K+-ATPase (E2-BeFx)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.05 Å

Oligo State

hetero-2-2-2-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: 4 residues within 4Å: Chain B: G.157, N.158, E.228, F.230 No protein-ligand interaction detected (PLIP)

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)(Non-covalent)

BEF.2: 11 residues within 4Å: Chain A: G.218, D.374, K.375, T.376, V.614, T.615, G.616, K.696, D.715, N.718 Ligands: MG.7 No protein-ligand interaction detected (PLIP) BEF.12: 9 residues within 4Å: Chain D: G.218, D.374, T.376, T.615, G.616, K.696, D.715, N.718 Ligands: MG.16 No protein-ligand interaction detected (PLIP)

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

1AT.3: 12 residues within 4Å: Chain A: V.942, F.943, G.946, M.947, K.948 Chain D: K.982, P.983, T.984, F.987 Chain E: Y.68 Chain F: Y.21 Ligands: CLR.19 12 PLIP interactions: 6 interactions with chain A, 5 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: A:V.942, A:F.943, D:F.987, D:F.987 Hydrogen bonds: A:M.947, A:M.947, A:K.948, A:K.948, D:K.982, D:T.984, D:T.984, E:Y.68

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 10 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 Chain D: V.998 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: D:V.998, B:T.53, B:V.56, A:F.865, A:P.991 Hydrogen bonds: A:T.984 CLR.11: 11 residues within 4Å: Chain A: W.929, Y.968, P.983, W.986, F.987, F.990 Chain C: V.26, G.29, G.30, F.33 Ligands: 1DS.5 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:V.26, C:F.33, C:F.33, C:F.33, A:W.929, A:Y.968, A:P.983, A:W.986, A:W.986, A:W.986, A:W.986, A:F.990 CLR.13: 9 residues within 4Å: Chain A: F.943 Chain D: F.865, E.873, T.984, C.988, P.991, L.995 Chain E: T.53, V.56 9 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: E:T.53, E:V.56, A:F.943, D:F.865, D:F.865, D:T.984, D:P.991, D:L.995 Hydrogen bonds: D:E.873 CLR.19: 10 residues within 4Å: Chain D: Y.968, P.983, W.986, F.987, F.990 Chain F: V.26, G.29, G.30, F.33 Ligands: 1AT.3 14 PLIP interactions: 9 interactions with chain D, 5 interactions with chain F Hydrophobic interactions: D:P.983, D:W.986, D:W.986, D:W.986, D:W.986, D:W.986, D:F.987, D:F.990, D:F.990, F:V.26, F:F.33, F:F.33, F:F.33 Hydrogen bonds: F:G.30

1 x 1DS: 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside(Non-covalent)

1DS.5: 11 residues within 4Å: Chain A: K.982, P.983, T.984, F.987 Chain B: Y.68 Chain C: Y.21 Chain D: F.943, G.946, M.947, K.948 Ligands: CLR.11 9 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:Y.68, B:Y.68, A:T.984, D:M.947, D:K.948, C:Y.21 Hydrophobic interactions: A:F.987, D:F.943 Salt bridges: D:K.948

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 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 MG.7: 4 residues within 4Å: Chain A: D.374, T.376, D.715 Ligands: BEF.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.374, A:D.374, A:T.376, A:T.376, A:D.715 MG.8: 5 residues within 4Å: Chain A: G.277, K.724, A.726, D.727, D.745 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.745, A:D.745, H2O.1, H2O.1 MG.14: 5 residues within 4Å: Chain D: A.328, E.332, N.781, E.784, D.809 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.784, D:D.809, H2O.1, H2O.1, H2O.1 MG.15: 5 residues within 4Å: Chain D: G.277, S.723, K.724, A.726, D.745 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.745, D:D.745, H2O.1 MG.16: 7 residues within 4Å: Chain D: D.374, T.376, G.377, T.378, D.715, D.719 Ligands: BEF.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.374, D:T.376, D:D.715

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.9: 3 residues within 4Å: Chain B: N.193, N.205, P.206 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.206 Hydrogen bonds: B:N.205, B:N.205 NAG.10: 1 residues within 4Å: Chain B: N.265 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain E: N.193, K.203 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.193, E:K.203 Salt bridges: E:K.203 NAG.18: 4 residues within 4Å: Chain E: N.158, E.228, F.230, Q.262 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:E.228, E:F.230 Hydrogen bonds: E:N.158, E:Q.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fruergaard, M.U. et al., The Na + ,K + -ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state. J.Biol.Chem. (2022)

Release Date

2022-11-23

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: AD
Sodium/potassium-transporting ATPase subunit beta-1: BE
FXYD domain-containing ion transport regulator: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

E
D

C
G

F
E

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Sodium/potassium-transporting ATPase subunit alpha-1

Sodium/potassium-transporting ATPase subunit beta-1

FXYD domain-containing ion transport regulator

Related Entries With Identical Sequence