SMTL ID : 5ylv.1

Crystal structure of the gastric proton pump complexed with SCH28080

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 8WX: 2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile(Non-covalent)

8WX.1: 16 residues within 4Å: Chain A: A.124, D.138, N.139, L.142, V.332, M.335, A.336, V.339, A.340, E.796, L.797, P.799, Y.800, L.810, L.812, C.814 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.124, A:L.142, A:V.332, A:M.335, A:A.336, A:V.339, A:A.340, A:Y.800, A:Y.800, A:L.810, A:L.812 Hydrogen bonds: A:L.812 pi-Stacking: A:Y.800

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: S.226, D.386, T.388, D.727, G.728, N.730 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.388, A:D.727

2 x CE1: O-DODECANYL OCTAETHYLENE GLYCOL(Non-covalent)

CE1.3: 8 residues within 4Å: Chain A: T.877, F.996, Q.997, L.1000, P.1004, F.1005 Chain B: C.57 Ligands: CE1.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.877, A:P.1004, A:F.1005 CE1.11: 6 residues within 4Å: Chain A: T.881, Q.997 Chain B: C.57, T.64, Y.72 Ligands: CE1.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.72

3 x RB: RUBIDIUM ION(Non-covalent)

RB.4: 5 residues within 4Å: Chain A: A.340, V.342, E.344, N.793, E.821 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.342 RB.5: 4 residues within 4Å: Chain A: L.735, K.736, A.738, D.757 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:K.736, A:A.738, A:D.757 RB.6: 3 residues within 4Å: Chain A: S.409, Q.419, T.420 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.409, A:S.409

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

NAG.7: 3 residues within 4Å: Chain B: N.98, Q.288, K.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.98, B:K.289 NAG.8: 2 residues within 4Å: Chain B: N.129, K.152 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: N.160, E.215, L.249 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.215, B:L.249 Hydrogen bonds: B:N.160, B:E.215

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

PCW.10: 15 residues within 4Å: Chain A: A.869, S.872, F.873, F.876, F.880, F.889, P.890, L.891, V.894 Chain B: F.54, I.58, Y.59, M.62, I.65, P.67 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.869, A:F.873, A:F.873, A:F.876, A:F.876, A:F.880, A:P.890, A:L.891, A:V.894, B:F.54, B:F.54, B:I.58, B:I.58, B:Y.59 Hydrogen bonds: A:L.891

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, K. et al., Crystal structures of the gastric proton pump. Nature (2018)

Release Date

2018-04-11

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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