SMTL ID : 8ijv.1

Cryo-EM structure of the gastric proton pump with bound DQ-02

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

PCW.1: 8 residues within 4Å: Chain A: Y.140, A.144, A.147, I.814, L.817, L.821, I.987, F.988 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.144, A:A.147, A:L.817, A:L.821, A:L.821 PCW.3: 14 residues within 4Å: Chain A: I.940, I.968, V.972, C.976, Y.980, M.991, P.992, R.994, F.995, W.998, M.1002 Chain B: D.75, Q.76 Ligands: PCW.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.940, A:I.968, A:V.972, A:V.972, A:V.972, A:Y.980, A:W.998, A:W.998 Hydrogen bonds: A:F.995 Water bridges: A:R.994 Salt bridges: A:R.994 PCW.4: 10 residues within 4Å: Chain A: Y.922, F.977, C.981, P.982, G.983, P.985, N.986, I.987, F.988 Ligands: PCW.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.977, A:F.977, A:F.977, A:I.987 Hydrogen bonds: A:G.983 PCW.5: 12 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 Ligands: CLR.11 14 PLIP interactions: 2 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:F.47, B:F.47, A:L.1007, A:V.1010, A:Y.1011, A:Y.1011, A:Y.1011, A:I.1014, A:I.1014, A:W.1027, A:W.1027, A:W.1027, A:W.1027 Hydrogen bonds: A:W.1026 PCW.7: 18 residues within 4Å: Chain A: I.801, 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 Ligands: CLR.12 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.801, A:F.875, A:F.879, A:L.890, A:L.890, A:V.893, B:Y.48, B:A.56, B:I.59, B:Y.60 Water bridges: A:L.890

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.225, D.385, T.387, D.726 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 PWI: 4-[[5-chloranyl-2-(4-chlorophenyl)phenyl]methoxy]-N-methyl-but-2-yn-1-amine(Non-covalent)

PWI.6: 19 residues within 4Å: Chain A: C.120, A.123, D.137, N.138, L.141, M.334, A.335, V.338, A.339, V.341, E.343, N.792, E.795, Y.799, L.811, G.812, C.813, I.816, E.820 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.141, A:A.335, A:V.338, A:Y.799 Halogen bonds: A:L.811

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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.102 Hydrogen bonds: B:N.255, B:Q.289 NAG.9: 2 residues within 4Å: Chain B: N.130, K.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.153 NAG.10: 4 residues within 4Å: Chain B: N.161, E.216, K.248, L.250 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.248, B:L.250 Hydrogen bonds: B:N.161, B:E.216

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 6 residues within 4Å: Chain A: W.1026 Chain B: W.39, L.42, A.46, V.49 Ligands: PCW.5 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.39, B:W.39, B:L.42, B:A.46, B:V.49, A:W.1026, A:W.1026 CLR.12: 8 residues within 4Å: Chain A: E.856, A.860 Chain B: R.32, I.40, S.41, Y.44, Y.48 Ligands: PCW.7 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.40, B:Y.44, B:Y.44, B:Y.44, B:Y.48, A:A.860 Hydrogen bonds: B:R.32, B:R.32 Water bridges: A:E.1030

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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