Cryo-EM structure of the gastric proton pump with bound DQ-02
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8ijv
Q-score: 0.687
Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A
Commun Biol (2023) 6 pp. 956-956 [ DOI: doi:10.1038/s42003-023-05334-8 Pubmed: 37726448 ]
- Potassium-transporting atpase subunit beta (33 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha (114 kDa, Protein from Sus scrofa)
- Hetero dimer of alpha and beta subunit (135 kDa, Complex from Sus scrofa)
- Cholesterol (386 Da, Ligand)
- 4-[[5-chloranyl-2-(4-chlorophenyl)phenyl]methoxy]-n-methyl-but-2-yn-1-amine (334 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
Cryo-EM structure of the gastric proton pump with bound DQ-06
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 8ijw
Q-score: 0.658
Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A
Commun Biol (2023) 6 pp. 956-956 [ DOI: doi:10.1038/s42003-023-05334-8 Pubmed: 37726448 ]
- Potassium-transporting atpase subunit beta (33 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha (114 kDa, Protein from Sus scrofa)
- N-methyl-1-[4-[(2-phenylmethoxycyclohexa-1,3-dien-1-yl)methoxy]cyclohexa-1,3-dien-1-yl]methanamine (337 Da, Ligand)
- Hetero dimer of alpha and beta subunit (135 kDa, Complex from Sus scrofa)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
Cryo-EM structure of the gastric proton pump with bound DQ-18
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 8ijx
Q-score: 0.68
Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A
Commun Biol (2023) 6 pp. 956-956 [ DOI: doi:10.1038/s42003-023-05334-8 Pubmed: 37726448 ]
- Potassium-transporting atpase subunit beta (33 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha (114 kDa, Protein from Sus scrofa)
- Hetero dimer of alpha and beta subunit (135 kDa, Complex from Sus scrofa)
- Cholesterol (386 Da, Ligand)
- 1-[4-[(5-chloranyl-2-phenylmethoxy-phenyl)methoxy]phenyl]-n-methyl-methanamine (367 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
Cryo-EM structure of the gastric proton pump with bound DQ-21
Resolution: 2.26 Å
EM Method: Single-particle
Fitted PDBs: 8jmn
Q-score: 0.67
Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A
Commun Biol (2023) 6 pp. 956-956 [ DOI: doi:10.1038/s42003-023-05334-8 Pubmed: 37726448 ]
- Potassium-transporting atpase subunit beta (33 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha (114 kDa, Protein from Sus scrofa)
- Hetero dimer of alpha and beta subunit (135 kDa, Complex from Sus scrofa)
- Cholesterol (386 Da, Ligand)
- 1-[4-[[2-[(4-chlorophenyl)methoxy]phenyl]methoxy]phenyl]-n-methyl-methanamine (367 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
Cryo-EM structure of the gastric proton pump complexed with revaprazan
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7w4a
Q-score: 0.536
Tanaka S, Morita M, Yamagishi T, Madapally HV, Hayashida K, Khandelia H, Gerle C, Shigematsu H, Oshima A, Abe K
J Med Chem (2022) 65 pp. 7843-7853 [ Pubmed: 35604136 DOI: doi:10.1021/acs.jmedchem.2c00338 ]
- Potassium-transporting atpase subunit beta (33 kDa, Protein from Sus scrofa)
- Gastric proton pump (135 kDa, Complex from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Potassium-transporting atpase alpha chain 1 (114 kDa, Protein from Sus scrofa)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- N-(4-fluorophenyl)-4,5-dimethyl-6-[(1r)-1-methyl-3,4-dihydro-1h-isoquinolin-2-yl]pyrimidin-2-amine (362 Da, Ligand)
- Sodium ion (22 Da, Ligand)