SMTL ID : 8jmn.1

Cryo-EM structure of the gastric proton pump with bound DQ-21

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: 13 residues within 4Å: Chain A: Y.140, L.143, A.144, A.147, V.148, V.151, I.814, L.817, F.818, L.821, C.822, I.987, F.988 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.143, A:A.144, A:A.147, A:V.148, A:V.151, A:L.817, A:F.818, A:F.818 Hydrogen bonds: A:I.987 PCW.3: 14 residues within 4Å: Chain A: M.937, I.940, V.972, C.976, Y.980, P.992, I.993, R.994, F.995, W.998, M.1002 Chain B: D.75, Q.76, K.78 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.940, A:V.972, A:Y.980, A:Y.980, A:Y.980, A:W.998 Hydrogen bonds: A:F.995 Water bridges: A:R.994 Salt bridges: A:R.994, B:D.75 PCW.4: 9 residues within 4Å: Chain A: C.822, C.973, I.974, F.977, P.982, G.983, P.985, I.987, F.988 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.974, A:F.977, A:F.977, A:F.977, A:F.977, A:I.987 Hydrogen bonds: A:G.983 PCW.5: 14 residues within 4Å: Chain A: L.1007, Y.1011, I.1014, G.1018, C.1022, P.1023, G.1024, S.1025, W.1026, W.1027 Chain B: Y.43, A.46, F.47 Ligands: CLR.11 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.1007, A:Y.1011, A:Y.1011, A:I.1014, A:W.1027, A:W.1027, A:W.1027, A:W.1027, B:Y.43, B:A.46, B:F.47 Hydrogen bonds: A:W.1026 PCW.7: 18 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, Y.60, M.63, I.66, P.68 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:Y.48, B:A.56, B:I.59, B:I.59, A:T.797, A:I.801, A:I.801, A:F.872, A:F.872, A:F.875, A:F.879, A:L.890, A:L.890, A:V.893 Water bridges: A:L.890

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.385, T.387, D.726, D.730 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 UOU: 1-[4-[[2-[(4-chlorophenyl)methoxy]phenyl]methoxy]phenyl]-N-methyl-methanamine(Non-covalent)

UOU.6: 20 residues within 4Å: Chain A: I.119, C.120, A.123, D.137, N.138, L.141, M.334, A.335, V.338, A.339, V.341, P.342, E.343, N.792, E.795, L.796, Y.799, L.811, I.816, E.820 12 PLIP interactions: 12 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:V.341 Water bridges: A:V.341, A:E.795 Halogen bonds: A:I.119

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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.102 Hydrogen bonds: B:N.255, B:Q.289, B:K.290 NAG.9: 2 residues within 4Å: Chain B: N.130, K.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.153 Water bridges: B:N.130 NAG.10: 4 residues within 4Å: Chain B: N.161, E.216, F.218, K.248 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.161, B:E.216

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 6 residues within 4Å: Chain A: W.1026 Chain B: W.39, L.42, Y.43, A.46 Ligands: PCW.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: 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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