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4UX1
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BU of 4ux1 by Molmil
Cryo-EM structure of antagonist-bound E2P gastric H,K-ATPase (SCH.E2. AlF)
Descriptor: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1, POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA
Authors:Abe, K, Tani, K, Fujiyoshi, Y.
Deposit date:2014-08-18
Release date:2014-09-17
Last modified:2014-11-12
Method:ELECTRON CRYSTALLOGRAPHY (8 Å)
Cite:Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating.
J.Biol.Chem., 289, 2014
3IXZ
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BU of 3ixz by Molmil
Pig gastric H+/K+-ATPase complexed with aluminium fluoride
Descriptor: Potassium-transporting ATPase alpha, Potassium-transporting ATPase subunit beta
Authors:Abe, K, Tani, K, Nishizawa, T, Fujiyoshi, Y.
Deposit date:2009-03-09
Release date:2009-06-23
Last modified:2024-02-21
Method:ELECTRON CRYSTALLOGRAPHY (6.5 Å)
Cite:Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycle
Embo J., 28, 2009
4UX2
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BU of 4ux2 by Molmil
Cryo-EM structure of antagonist-bound E2P gastric H,K-ATPase (SCH.E2. MgF)
Descriptor: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1, POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA
Authors:Abe, K, Tani, K, Fujiyoshi, Y.
Deposit date:2014-08-18
Release date:2014-09-17
Last modified:2014-11-12
Method:ELECTRON CRYSTALLOGRAPHY (7 Å)
Cite:Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating.
J.Biol.Chem., 289, 2014
6M5B
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BU of 6m5b by Molmil
X-ray crystal structure of cyclic-PIP and DNA complex in a reverse binding orientation
Descriptor: 1,2-ETHANEDIOL, 4-[[4-[(4-azanyl-1-methyl-pyrrol-2-yl)carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-~{N}-[2-[[(3~{S})-3-azanyl-4-oxidanylidene-butyl]carbamoyl]-1-methyl-imidazol-4-yl]-1-methyl-imidazole-2-carboxamide, DNA (5'-D(*CP*(CBR)P*AP*GP*GP*CP*CP*TP*GP*G)-3'), ...
Authors:Abe, K, Hirose, Y, Eki, H, Takeda, K, Bando, T, Endo, M, Sugiyama, H.
Deposit date:2020-03-10
Release date:2020-06-24
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.501 Å)
Cite:X-ray Crystal Structure of a Cyclic-PIP-DNA Complex in the Reverse-Binding Orientation.
J.Am.Chem.Soc., 142, 2020
5GZK
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BU of 5gzk by Molmil
Endo-beta-1,2-glucanase from Chitinophaga pinensis - sophorotriose and glucose complex
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, PENTAETHYLENE GLYCOL, ...
Authors:Abe, K, Nakajima, M, Arakawa, T, Fushinobu, S, Taguchi, H.
Deposit date:2016-09-28
Release date:2017-03-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family
J. Biol. Chem., 292, 2017
5GZH
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BU of 5gzh by Molmil
Endo-beta-1,2-glucanase from Chitinophaga pinensis - ligand free form
Descriptor: Endo-beta-1,2-glucanase, IODIDE ION, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
Authors:Abe, K, Nakajima, M, Arakawa, T, Fushinobu, S, Taguchi, H.
Deposit date:2016-09-28
Release date:2017-03-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family
J. Biol. Chem., 292, 2017
8IJM
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BU of 8ijm by Molmil
Cyo-EM structure of K794A non-gastric proton pump in Na+ bound E1AMPPCP state
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ...
Authors:Abe, K.
Deposit date:2023-02-27
Release date:2023-08-02
Last modified:2023-08-09
Method:ELECTRON MICROSCOPY (3.13 Å)
Cite:An unusual conformation from Na + -sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na + -binding.
Biochim Biophys Acta Mol Cell Res, 1870, 2023
8IJX
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BU of 8ijx by Molmil
Cryo-EM structure of the gastric proton pump with bound DQ-18
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 1-[4-[(5-chloranyl-2-phenylmethoxy-phenyl)methoxy]phenyl]-N-methyl-methanamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Abe, K, Yokoshima, S, Yoshimori, A.
Deposit date:2023-02-28
Release date:2023-08-30
Last modified:2023-10-04
Method:ELECTRON MICROSCOPY (2.08 Å)
Cite:Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
8IJV
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BU of 8ijv by Molmil
Cryo-EM structure of the gastric proton pump with bound DQ-02
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-[[5-chloranyl-2-(4-chlorophenyl)phenyl]methoxy]-N-methyl-but-2-yn-1-amine, ...
Authors:Abe, K, Yokoshima, S, Yoshimori, A.
Deposit date:2023-02-28
Release date:2023-08-30
Last modified:2023-10-04
Method:ELECTRON MICROSCOPY (2.1 Å)
Cite:Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
8JMN
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BU of 8jmn by Molmil
Cryo-EM structure of the gastric proton pump with bound DQ-21
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 1-[4-[[2-[(4-chlorophenyl)methoxy]phenyl]methoxy]phenyl]-N-methyl-methanamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Abe, K, Yokoshima, S, Yoshimori, A.
Deposit date:2023-06-05
Release date:2023-08-30
Last modified:2023-10-04
Method:ELECTRON MICROSCOPY (2.26 Å)
Cite:Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
8IJW
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BU of 8ijw by Molmil
Cryo-EM structure of the gastric proton pump with bound DQ-06
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ...
Authors:Abe, K, Yokoshima, S, Yoshimori, A.
Deposit date:2023-02-28
Release date:2023-08-30
Last modified:2023-10-04
Method:ELECTRON MICROSCOPY (2.19 Å)
Cite:Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
8IJL
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BU of 8ijl by Molmil
Cyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside, ...
Authors:Abe, K.
Deposit date:2023-02-27
Release date:2023-10-18
Method:ELECTRON MICROSCOPY (2.62 Å)
Cite:An unusual conformation from Na + -sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na + -binding.
Biochim Biophys Acta Mol Cell Res, 1870, 2023
7EFN
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BU of 7efn by Molmil
Crystal structure of the gastric proton pump K791S/E820D/Y340N/E936V in (BYK)E2BeF state
Descriptor: (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ...
Authors:Abe, K, Yamamoto, K, Irie, K.
Deposit date:2021-03-22
Release date:2021-09-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations.
Nat Commun, 12, 2021
7EFM
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BU of 7efm by Molmil
Crystal structure of the gastric proton pump K791S/E820D/Y340N in (BYK)E2BeF state
Descriptor: (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ...
Authors:Abe, K, Yamamoto, K, Irie, K.
Deposit date:2021-03-22
Release date:2021-09-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations.
Nat Commun, 12, 2021
7EFL
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BU of 7efl by Molmil
Crystal structure of the gastric proton pump K791S in (BYK)E2BeF state
Descriptor: (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ...
Authors:Abe, K, Yamamoto, K, Irie, K.
Deposit date:2021-03-22
Release date:2021-09-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations.
Nat Commun, 12, 2021
7ET1
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BU of 7et1 by Molmil
Cryo-EM structure of the gastric proton pump K791S/E820D/Y340N/E936V/Y799W mutant in K+-occluded (K+)E2-AlF state
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ...
Authors:Abe, K.
Deposit date:2021-05-12
Release date:2021-09-01
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations.
Nat Commun, 12, 2021
2XZB
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BU of 2xzb by Molmil
Pig Gastric H,K-ATPase with bound BeF and SCH28080
Descriptor: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1, POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA
Authors:Abe, K, Tani, K, Fujiyoshi, Y.
Deposit date:2010-11-24
Release date:2011-01-26
Last modified:2020-09-16
Method:ELECTRON CRYSTALLOGRAPHY (7 Å)
Cite:Conformational Rearrangement of Gastric H(+),K(+)- ATPase Induced by an Acid Suppressant.
Nat.Commun., 2, 2011
2YN9
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BU of 2yn9 by Molmil
Cryo-EM structure of gastric H+,K+-ATPase with bound rubidium
Descriptor: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1, POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA
Authors:Abe, K, Tani, K, Friedrich, T, Fujiyoshi, Y.
Deposit date:2012-10-13
Release date:2012-11-07
Last modified:2014-07-16
Method:ELECTRON CRYSTALLOGRAPHY (8 Å)
Cite:Cryo-Em Structure of Gastric H+,K+-ATPase with a Single Occupied Cation-Binding Site.
Proc.Natl.Acad.Sci.USA, 109, 2012
5Y0B
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BU of 5y0b by Molmil
PIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99
Descriptor: Potassium-transporting ATPase alpha chain 1, Potassium-transporting ATPase subunit beta
Authors:Abe, K, Shimokawa, J, Natio, M, Munson, K, Vagin, O, Sachs, G, Suzuki, H, Tani, K, Fujiyoshi, Y.
Deposit date:2017-07-16
Release date:2017-08-09
Method:ELECTRON CRYSTALLOGRAPHY (6.7 Å)
Cite:The cryo-EM structure of gastric H(+),K(+)-ATPase with bound BYK99, a high-affinity member of K(+)-competitive, imidazo[1,2-a]pyridine inhibitors
Sci Rep, 7, 2017
5YLV
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BU of 5ylv by Molmil
Crystal structure of the gastric proton pump complexed with SCH28080
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Abe, K, Irie, K, Nakanishi, H, Fujiyoshi, Y.
Deposit date:2017-10-19
Release date:2018-04-11
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.79977775 Å)
Cite:Crystal structures of the gastric proton pump
Nature, 556, 2018
5YLU
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BU of 5ylu by Molmil
Crystal structure of the gastric proton pump complexed with vonoprazan
Descriptor: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Abe, K, Irie, K, Nakanishi, H, Fujiyoshi, Y.
Deposit date:2017-10-19
Release date:2018-04-11
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.79988956 Å)
Cite:Crystal structures of the gastric proton pump
Nature, 556, 2018
5YSD
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BU of 5ysd by Molmil
Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Lin1841 protein, MAGNESIUM ION, ...
Authors:Abe, K, Nakajima, M, Taguchi, H, Arakawa, T, Fushinobu, S.
Deposit date:2017-11-14
Release date:2018-05-02
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
J. Biol. Chem., 293, 2018
5YSF
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BU of 5ysf by Molmil
Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophoropentaose
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Lin1841 protein, MAGNESIUM ION, ...
Authors:Abe, K, Nakajima, M, Taguchi, H, Arakawa, T, Fushinobu, S.
Deposit date:2017-11-14
Release date:2018-05-02
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
J. Biol. Chem., 293, 2018
5YSE
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BU of 5yse by Molmil
Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotetraose
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Lin1841 protein, MAGNESIUM ION, ...
Authors:Abe, K, Nakajima, M, Taguchi, H, Arakawa, T, Fushinobu, S.
Deposit date:2017-11-14
Release date:2018-05-02
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
J. Biol. Chem., 293, 2018
5YSB
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BU of 5ysb by Molmil
Crystal structure of beta-1,2-glucooligosaccharide binding protein in ligand-free form
Descriptor: DI(HYDROXYETHYL)ETHER, Lin1841 protein, ZINC ION
Authors:Abe, K, Nakajima, M, Taguchi, H, Arakawa, T, Fushinobu, S.
Deposit date:2017-11-13
Release date:2018-05-02
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
J. Biol. Chem., 293, 2018

 

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