SMTL ID : 8ijx.1

Cryo-EM structure of the gastric proton pump with bound DQ-18

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

PCW.1: 12 residues within 4Å: Chain A: Y.140, L.143, A.144, A.147, V.148, I.814, L.817, F.818, L.821, C.822, I.987, F.988 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.143, A:L.143, A:A.144, A:A.147, A:V.148, A:L.817, A:F.818, A:F.818, A:F.818, A:L.821, A:L.821 PCW.3: 15 residues within 4Å: Chain A: M.937, I.940, I.968, 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 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Salt bridges: B:D.75, A:R.994 Hydrophobic interactions: A:I.940, A:I.968, A:Y.980, A:F.995, A:W.998 Hydrogen bonds: A:F.995 PCW.4: 9 residues within 4Å: Chain A: F.818, C.973, F.977, C.981, P.982, G.983, P.985, I.987, F.988 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.818, A:F.977, A:F.977, A:F.977, A:P.982, A:I.987 PCW.5: 14 residues within 4Å: Chain A: L.1007, V.1010, Y.1011, I.1014, G.1018, C.1022, G.1024, S.1025, W.1026, W.1027 Chain B: Y.43, F.47, V.50 Ligands: CLR.12 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.1007, A:V.1010, A:I.1014, A:W.1027, A:W.1027, A:W.1027, A:W.1027, B:F.47, B:F.47, B:V.50 Hydrogen bonds: A:W.1026 Water bridges: A:S.1025, A:S.1025 PCW.7: 11 residues within 4Å: Chain A: A.347, V.351, R.359, I.825, F.826, V.829, Y.833, K.835, I.963, I.966, F.970 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.347, A:V.351, A:V.351, A:F.826, A:F.826, A:F.826, A:F.826, A:V.829, A:Y.833, A:I.963, A:I.966, A:F.970, A:F.970 PCW.8: 17 residues within 4Å: Chain A: T.797, 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, M.63, I.66, P.68 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.797, A:I.801, A:F.872, A:F.872, A:F.872, A:F.879, A:L.890, A:V.893, B:Y.48, B:I.59, B:I.59 Water bridges: A:L.890

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: 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 PZ0: 1-[4-[(5-chloranyl-2-phenylmethoxy-phenyl)methoxy]phenyl]-N-methyl-methanamine(Non-covalent)

PZ0.6: 22 residues within 4Å: Chain A: C.120, A.123, Q.127, D.137, N.138, L.141, V.331, M.334, A.335, V.338, A.339, V.341, P.342, E.343, N.792, E.795, Y.799, L.811, G.812, C.813, I.816, E.820 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.123, A:D.137, A:L.141, A:A.335, A:V.338, A:A.339, A:A.339, A:E.795, A:Y.799, A:I.816, A:I.816 Hydrogen bonds: A:V.341, A:E.795 Water bridges: A:V.341 Halogen bonds: A:L.811

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

NAG.9: 6 residues within 4Å: Chain B: N.99, S.101, D.102, N.255, Q.289, K.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.101, B:N.255 NAG.10: 1 residues within 4Å: Chain B: N.130 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain B: N.161, E.216, K.248 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.248 Hydrogen bonds: B:N.161, B:E.216

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.12: 6 residues within 4Å: Chain A: W.1026 Chain B: W.39, L.42, Y.43, A.46 Ligands: PCW.5 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.39, B:W.39, B:W.39, B:W.39, B:L.42, B:Y.43, B:A.46, A:W.1026, A:W.1026, A:W.1026

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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