SMTL ID : 8ijw.1

Cryo-EM structure of the gastric proton pump with bound DQ-06

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

PCW.1: 19 residues within 4Å: Chain A: T.797, I.801, A.868, S.871, F.872, F.875, F.879, F.888, P.889, L.890, V.893 Chain B: Y.48, S.52, A.56, I.59, Y.60, M.63, I.66, P.68 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.48, B:A.56, B:Y.60, A:T.797, A:I.801, A:A.868, A:F.875, A:L.890 Water bridges: A:L.890 PCW.2: 14 residues within 4Å: Chain A: D.136, Y.140, L.143, A.144, A.147, V.148, V.151, A.347, L.817, F.818, L.821, I.825, I.987, F.988 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.143, A:A.147, A:V.148, A:V.151, A:V.151, A:A.347, A:L.817, A:L.817, A:F.818, A:L.821, A:I.825 Hydrogen bonds: A:Y.140, A:I.987 Salt bridges: A:D.136 PCW.5: 13 residues within 4Å: Chain A: M.937, V.972, C.976, Y.980, M.991, P.992, I.993, R.994, F.995, W.998, M.1002 Chain B: D.75, Q.76 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.980, A:W.998, A:W.998 Hydrogen bonds: A:F.995 Water bridges: A:R.994 Salt bridges: A:R.994, B:D.75 PCW.6: 10 residues within 4Å: Chain A: Y.922, I.974, F.977, P.982, G.983, M.984, P.985, N.986, I.987, F.988 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.974, A:F.977, A:F.977, A:F.977, A:P.982, A:I.987 PCW.7: 13 residues within 4Å: Chain A: L.1007, V.1010, Y.1011, I.1014, C.1022, S.1025, W.1026, W.1027, Q.1029 Chain B: Y.43, F.47, M.51 Ligands: CLR.11 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:F.47, B:F.47, A:L.1007, A:V.1010, A:Y.1011, A:I.1014, A:W.1027, A:W.1027, A:W.1027, A:W.1027 Hydrogen bonds: A:W.1026

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.385, T.387, D.726, G.727 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.387, A:D.726, H2O.1, H2O.1

1 x PXR: N-methyl-1-[4-[(2-phenylmethoxycyclohexa-1,3-dien-1-yl)methoxy]cyclohexa-1,3-dien-1-yl]methanamine(Non-covalent)

PXR.4: 19 residues within 4Å: Chain A: C.120, A.123, D.137, N.138, L.141, V.331, A.335, A.339, V.341, P.342, E.343, N.792, E.795, L.796, Y.799, L.811, C.813, I.816, E.820 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.123, A:L.141, A:A.335, A:A.339, A:E.795, A:Y.799, A:Y.799, A:I.816 Hydrogen bonds: A:A.339 Water bridges: A:E.795

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

NAG.8: 6 residues within 4Å: Chain B: N.99, S.101, D.102, N.255, Q.289, K.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255 NAG.9: 1 residues within 4Å: Chain B: N.130 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain B: N.161, E.216, K.248, L.250 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.216, B:L.250 Hydrogen bonds: B:N.161, B:E.216, B:E.216

2 x CLR: CHOLESTEROL(Non-covalent)(Covalent)

CLR.11: 6 residues within 4Å: Chain A: W.1026 Chain B: W.39, L.42, Y.43, A.46 Ligands: PCW.7 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.39, B:W.39, B:W.39, B:L.42, B:A.46, A:W.1026, A:W.1026, A:W.1026 CLR.12: 6 residues within 4Å: Chain A: E.856, A.860 Chain B: R.32, W.37, I.40, Y.44 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.37, B:W.37, B:I.40, B:Y.44, B:Y.44 Hydrogen bonds: B:R.32, B:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, K. et al., Deep learning driven de novo drug design based on gastric proton pump structures. Commun Biol (2023)

Release Date

2023-08-30

Peptides

Sodium/potassium-transporting ATPase subunit alpha: 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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Sodium/potassium-transporting ATPase subunit alpha

Potassium-transporting ATPase subunit beta

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