SMTL ID : 5ylu.1

Crystal structure of the gastric proton pump complexed with vonoprazan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x HKT: 1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine(Non-covalent)

HKT.1: 13 residues within 4Å: Chain A: N.139, L.142, A.336, V.339, A.340, V.342, E.344, E.796, L.797, Y.800, L.812, C.814, I.817 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.142, A:L.142, A:A.336, A:Y.800, A:I.817, A:I.817 Hydrogen bonds: A:A.340

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

PCW.2: 15 residues within 4Å: Chain A: T.798, S.872, F.873, F.876, F.880, P.890, L.891 Chain B: Y.47, S.51, F.54, A.55, I.58, Y.59, M.62, I.65 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.798, A:F.873, A:F.876, B:Y.47, B:F.54, B:F.54, B:Y.59 Hydrogen bonds: A:L.891 PCW.3: 11 residues within 4Å: Chain A: T.135, Y.141, L.144, A.145, A.148, V.149, L.818, F.819, N.987, I.988, N.990 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.141, A:Y.141, A:L.144, A:A.145, A:V.149, A:L.818, A:F.819 Hydrogen bonds: A:Y.141, A:N.987, A:N.990

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: S.226, D.386, T.388, D.727, N.730 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.388, A:D.727, A:D.727

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

CE1.5: 7 residues within 4Å: Chain A: R.995, F.996, L.1000, V.1001, P.1004 Chain B: C.57 Ligands: CE1.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1000, A:V.1001 CE1.9: 7 residues within 4Å: Chain A: Q.885, Q.997 Chain B: C.57, L.61, T.64, Y.72 Ligands: CE1.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.61

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

NAG.6: 3 residues within 4Å: Chain B: N.98, D.101, K.289 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.129, T.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.129 NAG.8: 2 residues within 4Å: Chain B: N.160, E.215 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.215 Hydrogen bonds: B:N.160

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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