SMTL ID : 7w48.1

Crystal structure of the gastric proton pump complexed with PF-03716556

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: S.226, D.386, T.388, D.727, G.728, N.730, D.731 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.226, A:T.388, A:D.727, A:D.727

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

CE1.2: 10 residues within 4Å: Chain A: T.877, I.994, R.995, F.996, Q.997, L.1000, V.1001, P.1004 Chain B: C.58 Ligands: CE1.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.877, A:L.1000, A:V.1001 Hydrogen bonds: A:Q.997 CE1.6: 9 residues within 4Å: Chain A: T.881, Q.885, Q.997 Chain B: C.58, V.61, L.62, T.65, Y.73 Ligands: CE1.2 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.881, B:V.61, B:L.62, B:T.65 Hydrogen bonds: A:Q.997, B:Y.73

3 x RB: RUBIDIUM ION(Non-covalent)

RB.3: 4 residues within 4Å: Chain A: V.339, A.340, E.344, I.817 No protein-ligand interaction detected (PLIP) RB.4: 5 residues within 4Å: Chain A: N.289, 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.5: 3 residues within 4Å: Chain A: S.409, Q.419, T.420 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.409

1 x 8BZ: N-(2-hydroxyethyl)-N,2-dimethyl-8-[[(4R)-5-methyl-3,4-dihydro-2H-chromen-4-yl]amino]imidazo[1,2-a]pyridine-6-carboxamide(Non-covalent)

8BZ.7: 15 residues within 4Å: Chain A: A.124, Q.128, D.138, N.139, V.332, A.336, V.339, A.340, L.797, Y.800, L.810, L.812, G.813, C.814, Y.929 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.124, A:V.332, A:A.336, A:A.340, A:L.797, A:Y.800, A:Y.800 Hydrogen bonds: A:N.139, A:C.814

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

NAG.8: 5 residues within 4Å: Chain B: N.99, S.101, D.102, Q.289, K.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.99, B:K.290 NAG.9: 1 residues within 4Å: Chain B: N.130 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain B: N.161, E.216 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.216 Hydrogen bonds: B:E.216

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

PCW.11: 17 residues within 4Å: Chain A: T.798, S.872, F.873, F.876, F.880, F.889, P.890, L.891, V.894 Chain B: S.52, F.55, I.59, Y.60, M.63, R.64, I.66, P.68 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.798, A:F.873, A:F.876, A:F.876, A:F.876, A:F.880, A:P.890, A:L.891, A:V.894, B:F.55, B:F.55, B:I.59, B:Y.60 Hydrogen bonds: A:L.891

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, S. et al., Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J.Med.Chem. (2022)

Release Date

2022-01-05

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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