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

Rb+-bound E2-MgF state of the gastric proton pump (Wild-type)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MF4: TETRAFLUOROMAGNESATE(2-)(Non-covalent)

MF4.1: 13 residues within 4Å: Chain A: T.182, G.183, E.184, D.339, K.340, T.341, T.580, G.581, D.582, K.661, D.680, N.683 Ligands: MG.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.339

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.183, D.339, T.341, D.680 Ligands: MF4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.341, A:D.680, A:D.680

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 8 residues within 4Å: Chain A: E.810, A.814, F.818 Chain B: R.31, W.36, I.39, S.40, Y.43 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.814, A:F.818, A:F.818, B:W.36, B:I.39, B:Y.43 Hydrogen bonds: B:R.31

3 x K: POTASSIUM ION(Non-covalent)

K.4: 1 residues within 4Å: Chain A: A.700 No protein-ligand interaction detected (PLIP) K.5: 4 residues within 4Å: Chain A: L.688, K.689, A.691, D.710 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:K.689, A:A.691, A:D.710, A:D.710 K.6: 8 residues within 4Å: Chain A: V.292, A.293, V.295, E.297, N.746, E.749, I.770, E.774 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.292, A:V.295, A:E.297, A:E.749

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

NAG.7: 1 residues within 4Å: Chain B: N.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.192 NAG.8: 3 residues within 4Å: Chain B: P.144, N.145, H.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamamoto, K. et al., A single K + -binding site in the crystal structure of the gastric proton pump. Elife (2019)

Release Date

2019-08-14

Peptides

Potassium-transporting ATPase alpha chain 1: A
Potassium-transporting ATPase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Potassium-transporting ATPase alpha chain 1

Potassium-transporting ATPase subunit beta

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