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8IBT
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Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E318S mutant in complex with lacto-N-tetraose
分子名称: Beta-galactosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
著者Hidaka, M, Fushinobu, S, Gotoh, A, Katayama, T.
登録日2023-02-10
公開日2023-06-07
最終更新日2023-12-20
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses.
Microbiome Res Rep, 2, 2023
8IBS
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Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E160A/E318A mutant in complex with galactose
分子名称: Beta-galactosidase, alpha-D-galactopyranose
著者Hidaka, M, Fushinobu, S, Gotoh, A, Katayama, T.
登録日2023-02-10
公開日2023-06-07
最終更新日2023-12-20
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses.
Microbiome Res Rep, 2, 2023
7WDT
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6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S
分子名称: 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose, Beta-N-acetylhexosaminidase, ...
著者Yamada, C, Kashima, T, Fushinobu, S, Katoh, T, Katayama, T.
登録日2021-12-22
公開日2022-12-28
最終更新日2023-06-14
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
7WDU
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6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S
分子名称: Beta-N-acetylhexosaminidase, CALCIUM ION, [[(3R,4R,5S,6R)-3-acetamido-4,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-2-ylidene]amino] N-phenylcarbamate
著者Kashima, T, Yamada, C, Fushinobu, S, Katoh, T, Katayama, T.
登録日2021-12-22
公開日2022-12-28
最終更新日2023-06-14
実験手法X-RAY DIFFRACTION (2.23 Å)
主引用文献A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
7XMB
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Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Nishida, Y, Shinzawa-Itoh, K, Mizuno, N, Kumasaka, T, Yoshikawa, S, Tsukihara, T, Shintani, Y, Takashima, S.
登録日2022-04-25
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
7XMC
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Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO
分子名称: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, COPPER (II) ION, Cytochrome bo(3) ubiquinol oxidase subunit 1, ...
著者Nishida, Y, Shigematsu, H, Iwamoto, T, Takashima, S, Shintani, Y.
登録日2022-04-25
公開日2022-12-21
最終更新日2024-07-03
実験手法ELECTRON MICROSCOPY (3.09 Å)
主引用文献Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
7XMD
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Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4
分子名称: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, COPPER (II) ION, Cytochrome bo(3) ubiquinol oxidase subunit 1, ...
著者Nishida, Y, Shigematsu, H, Iwamoto, T, Takashima, S, Shintani, Y.
登録日2022-04-25
公開日2022-12-21
最終更新日2024-07-03
実験手法ELECTRON MICROSCOPY (2.99 Å)
主引用文献Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
7XMA
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Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Nishida, Y, Shinzawa-Itoh, K, Mizuno, N, Kumasaka, T, Yoshikawa, S, Tsukihara, T, Takashima, S, Shintani, Y.
登録日2022-04-25
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
5GJF
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Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 3
分子名称: N-(2-isopropoxy-4-(4-methylpiperazine-1-carbonyl)phenyl)-2-(3-(3-phenylureido)phenyl)thiazole-4-carboxamide, TAK1 kinase - TAB1 chimera fusion protein
著者Irie, M, Nakamura, M, Fukami, T.A, Matsuura, T, Morishima, K.
登録日2016-06-29
公開日2016-11-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.89 Å)
主引用文献Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)
Chem.Pharm.Bull., 64, 2016
5GJG
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Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 4
分子名称: N-(2-isopropoxy-4-(4-methylpiperazine-1-carbonyl)phenyl)-2-(3-(phenylcarbamoyl)phenyl)thiazole-4-carboxamide, TAK1 kinase - TAB1 chimera fusion protein
著者Irie, M, Nakamura, M, Fukami, T.A, Matsuura, T, Morishima, K.
登録日2016-06-29
公開日2016-11-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.61 Å)
主引用文献Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)
Chem.Pharm.Bull., 64, 2016
5GJD
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BU of 5gjd by Molmil
Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 2
分子名称: 1-(4-((1H-pyrrolo[2,3-b]pyridin-4-yl)oxy)phenyl)-3-(5-(4-methylpiperazin-1-yl)naphthalen-2-yl)urea, TAK1 kinase - TAB1 chimera fusion protein
著者Irie, M, Nakamura, M, Fukami, T.A, Matsuura, T, Morishima, K.
登録日2016-06-29
公開日2016-11-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.79 Å)
主引用文献Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)
Chem.Pharm.Bull., 64, 2016
5JGB
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Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 10
分子名称: N-(2-methoxy-4-{[3-(4-methylpiperazin-1-yl)propyl]carbamoyl}phenyl)-4-oxo-3,4-dihydrothieno[3,2-d]pyrimidine-7-carboxamide, TAK1 kinase - TAB1 chimera fusion protein
著者Irie, M, Nakamura, M, Fukami, T.A, Matsuura, T, Morishima, K.
登録日2016-04-20
公開日2016-07-27
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Discovery of a potent and highly selective transforming growth factor beta receptor-associated kinase 1 (TAK1) inhibitor by structure based drug design (SBDD)
Bioorg.Med.Chem., 24, 2016
6BPL
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E. coli MsbA in complex with LPS and inhibitor G907
分子名称: (2E)-3-{6-[(1S)-1-(2-chloro-6-cyclopropylphenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE, 2-amino-2-deoxy-alpha-D-glucopyranose, ...
著者Ho, H, Koth, C.M, Payandeh, J.
登録日2017-11-23
公開日2018-05-02
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (2.908 Å)
主引用文献Structural basis for dual-mode inhibition of the ABC transporter MsbA.
Nature, 557, 2018
6BPP
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E. coli MsbA in complex with LPS and inhibitor G092
分子名称: (2E)-3-{6-[(1S)-1-(3-amino-2,6-dichlorophenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid, 1,2-Distearoyl-sn-glycerophosphoethanolamine, 3-HYDROXY-TETRADECANOIC ACID, ...
著者Ho, H, Koth, C.M, Payandeh, J.
登録日2017-11-24
公開日2018-05-02
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.92 Å)
主引用文献Structural basis for dual-mode inhibition of the ABC transporter MsbA.
Nature, 557, 2018
5V7T
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crystal structure of PARP14 bound to N-{4-[4-(diphenylmethoxy)piperidin-1-yl]butyl}[1,2,4]triazolo[4,3-b]pyridazin-6-amine inhibitor
分子名称: N-{4-[4-(diphenylmethoxy)piperidin-1-yl]butyl}[1,2,4]triazolo[4,3-b]pyridazin-6-amine, Poly [ADP-ribose] polymerase 14
著者saikatendu, k.s, Hirozane, M.
登録日2017-03-20
公開日2017-05-03
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation.
Biochem. Biophys. Res. Commun., 486, 2017
5V7W
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Crystal structure of human PARP14 bound to 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one inhibitor
分子名称: 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one, Poly [ADP-ribose] polymerase 14
著者saikatendu, k.s, Hirozane, M.
登録日2017-03-20
公開日2017-05-10
最終更新日2018-11-14
実験手法X-RAY DIFFRACTION (2.65 Å)
主引用文献Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation.
Biochem. Biophys. Res. Commun., 486, 2017
3ONF
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Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with cordycepin
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 3'-DEOXYADENOSINE, Adenosylhomocysteinase, ...
著者Brzezinski, K, Jaskolski, M.
登録日2010-08-28
公開日2011-08-31
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Acta Crystallogr.,Sect.D, 68, 2012
3OND
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Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenosine
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ADENOSINE, Adenosylhomocysteinase, ...
著者Brzezinski, K, Jaskolski, M.
登録日2010-08-28
公開日2011-08-31
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (1.17 Å)
主引用文献High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Acta Crystallogr.,Sect.D, 68, 2012
1AS6
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STRUCTURE OF NITRITE BOUND TO OXIDIZED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE
分子名称: COPPER (II) ION, NITRITE ION, NITRITE REDUCTASE
著者Murphy, M.E.P, Adman, E.T, Turley, S.
登録日1997-08-13
公開日1998-02-25
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.
J.Biol.Chem., 272, 1997
1AQ8
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STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE REDUCED WITH ASCORBATE
分子名称: COPPER (II) ION, NITRITE REDUCTASE
著者Murphy, M.E.P, Adman, E.T, Turley, S.
登録日1997-08-07
公開日1998-02-25
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.
J.Biol.Chem., 272, 1997
1AS8
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STRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE
分子名称: COPPER (II) ION, NITRITE ION, NITRITE REDUCTASE
著者Murphy, M.E.P, Adman, E.T, Turley, S.
登録日1997-08-13
公開日1998-02-25
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.
J.Biol.Chem., 272, 1997
1AS7
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BU of 1as7 by Molmil
STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE
分子名称: COPPER (II) ION, NITRITE REDUCTASE
著者Murphy, M.E.P, Adman, E.T, Turley, S.
登録日1997-08-13
公開日1998-02-25
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.
J.Biol.Chem., 272, 1997
7XI9
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Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
分子名称: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3'), DNA (cytosine-5)-methyltransferase 1, ...
著者Onoda, H, Kikuchi, A, Kori, S, Yoshimi, S, Yamagata, A, Arita, K.
登録日2022-04-12
公開日2022-11-30
最終更新日2024-07-03
実験手法ELECTRON MICROSCOPY (2.52 Å)
主引用文献Structural basis for activation of DNMT1.
Nat Commun, 13, 2022
7XIB
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Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)
分子名称: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3'), DNA (cytosine-5)-methyltransferase 1, ...
著者Onoda, H, Kikuchi, A, Kori, S, Yoshimi, S, Yamagata, A, Arita, K.
登録日2022-04-12
公開日2022-11-30
最終更新日2024-07-03
実験手法ELECTRON MICROSCOPY (2.23 Å)
主引用文献Structural basis for activation of DNMT1.
Nat Commun, 13, 2022
3ONE
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Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenine
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ADENINE, Adenosylhomocysteinase, ...
著者Brzezinski, K, Jaskolski, M.
登録日2010-08-28
公開日2011-08-31
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Acta Crystallogr.,Sect.D, 68, 2012

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