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PDB: 61 件
7YQ2
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Crystal structure of photosystem II expressing psbA2 gene only
分子名称: (3R)-beta,beta-caroten-3-ol, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ...
著者Nakajima, Y, Suga, M, Shen, J.R.
登録日2022-08-05
公開日2022-11-30
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit.
J.Biol.Chem., 298, 2022
7YQ7
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Crystal structure of photosystem II expressing psbA3 gene only
分子名称: (3R)-beta,beta-caroten-3-ol, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ...
著者Nakajima, Y, Suga, M, Shen, J.R.
登録日2022-08-05
公開日2022-11-30
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit.
J.Biol.Chem., 298, 2022
2DCM
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BU of 2dcm by Molmil
The Crystal Structure of S603A Mutated Prolyl Tripeptidyl Aminopeptidase Complexed with Substrate
分子名称: GLYCYLALANYL-N-2-NAPHTHYL-L-PROLINEAMIDE, dipeptidyl aminopeptidase IV, putative
著者Nakajima, Y, Ito, K, Xu, Y, Yamada, N, Onohara, Y, Yoshimoto, T.
登録日2006-01-09
公開日2006-09-19
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Crystal Structure and Mechanism of Tripeptidyl Activity of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
J.Mol.Biol., 362, 2006
1IS2
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Crystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver
分子名称: FLAVIN-ADENINE DINUCLEOTIDE, acyl-CoA oxidase
著者Nakajima, Y, Miyahara, I, Hirotsu, K.
登録日2001-11-07
公開日2002-04-10
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase.
J.Biochem., 131, 2002
1V93
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5,10-Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8
分子名称: 1,4-DIETHYLENE DIOXIDE, 5,10-Methylenetetrahydrofolate reductase, FLAVIN-ADENINE DINUCLEOTIDE
著者Nakajima, Y, Miyahara, I, Hirotsu, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2004-01-20
公開日2004-02-03
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal Structure of 5,10-Methylenetetrahydrofolate reductase from Thermus thermophilus HB8
To be Published
2D5L
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Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
分子名称: SULFATE ION, dipeptidyl aminopeptidase IV, putative
著者Nakajima, Y, Ito, K, Xu, Y, Yamada, N, Onohara, Y, Yoshimoto, T.
登録日2005-11-02
公開日2006-09-19
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal Structure and Mechanism of Tripeptidyl Activity of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
J.Mol.Biol., 362, 2006
1X2E
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The crystal structure of prolyl aminopeptidase complexed with Ala-TBODA
分子名称: (2S)-2-AMINO-1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)PROPAN-1-ONE, Proline iminopeptidase
著者Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T.
登録日2005-04-22
公開日2006-05-09
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
J.Bacteriol., 188, 2006
1X2B
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The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA
分子名称: 1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-2-(METHYLAMINO)ETHANONE, Proline iminopeptidase
著者Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T.
登録日2005-04-22
公開日2006-05-09
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
J.Bacteriol., 188, 2006
2DQ6
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Crystal Structure of Aminopeptidase N from Escherichia coli
分子名称: Aminopeptidase N, SULFATE ION, ZINC ION
著者Nakajima, Y, Onohara, Y, Ito, K, Yoshimoto, T.
登録日2006-05-22
公開日2006-08-01
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli: Crystal structure and conformational change of the methionine 260 residue involved in substrate recognition
J.Biol.Chem., 281, 2006
7VKF
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BU of 7vkf by Molmil
Reduced enzyme of FAD-dpendent Glucose Dehydrogenase complex with D-glucono-1,5-lactone at pH8.5
分子名称: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, D-glucono-1,5-lactone, DIHYDROFLAVINE-ADENINE DINUCLEOTIDE, ...
著者Nakajima, Y, Nishiya, Y, Ito, K.
登録日2021-09-29
公開日2022-10-05
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
7VKD
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Reduced enzyme of FAD-dpendent Glucose Dehydrogenase at pH6.5
分子名称: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE, GMC oxidoreductase
著者Nakajima, Y, Nishiya, Y, Ito, K.
登録日2021-09-29
公開日2022-10-05
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.58 Å)
主引用文献Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
3A6J
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E122Q mutant creatininase complexed with creatine
分子名称: Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-09-02
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6D
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Creatininase complexed with 1-methylguanidine
分子名称: 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-08-31
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
2ECF
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Crystal Structure of Dipeptidyl Aminopeptidase IV from Stenotrophomonas maltophilia
分子名称: Dipeptidyl peptidase IV
著者Nakajima, Y, Ito, K, Yoshimoto, T.
登録日2007-02-13
公開日2008-02-26
最終更新日2011-07-13
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue
J.Bacteriol., 190, 2008
3A6E
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W174F mutant creatininase, type I
分子名称: CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-08-31
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6L
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E122Q mutant creatininase, Zn-Zn type
分子名称: CHLORIDE ION, Creatinine amidohydrolase, ZINC ION
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-09-02
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6H
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W154A mutant creatininase
分子名称: CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-08-31
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6K
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The E122Q mutant creatininase, Mn-Zn type
分子名称: CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-09-02
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6F
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W174F mutant creatininase, Type II
分子名称: CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-08-31
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.78 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6G
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W154F mutant creatininase
分子名称: Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-08-31
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
7VZS
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FAD-dpendent Glucose Dehydrogenase complexed with an inhibitor at pH7.56
分子名称: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, D-glucal, FLAVIN-ADENINE DINUCLEOTIDE, ...
著者Nakajima, Y.
登録日2021-11-16
公開日2022-11-16
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
7VZP
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FAD-dpendent Glucose Dehydrogenase from Aspergillus oryzae
分子名称: FLAVIN-ADENINE DINUCLEOTIDE, GMC oxidoreductase, PENTAETHYLENE GLYCOL
著者Nakajima, Y.
登録日2021-11-16
公開日2022-11-16
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.2 Å)
主引用文献Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
5ZZN
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Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus
分子名称: (3R)-beta,beta-caroten-3-ol, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ...
著者Nakajima, Y, Umena, Y, Nagao, R, Endo, K, Kobayashi, K, Akita, F, Suga, M, Wada, H, Noguchi, T, Shen, J.R.
登録日2018-06-03
公開日2018-08-01
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.
J. Biol. Chem., 293, 2018
2ZXG
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Aminopeptidase N complexed with the aminophosphinic inhibitor of PL250, a transition state analogue
分子名称: Aminopeptidase N, GLYCEROL, N-{(2S)-3-[(1R)-1-aminoethyl](hydroxy)phosphoryl-2-benzylpropanoyl}-L-phenylalanine, ...
著者Nakajima, Y, Ito, K, Yoshimoto, T.
登録日2008-12-24
公開日2009-08-25
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Structure of aminopeptidase N from Escherichia coli complexed with the transition-state analogue aminophosphinic inhibitor PL250
Acta Crystallogr.,Sect.D, 65, 2009
1WM1
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Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA
分子名称: (5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)[(2R)-PYRROLIDIN-2-YL]METHANONE, Proline iminopeptidase
著者Nakajima, Y, Inoue, T, Ito, K, Tozaka, T, Hatakeyama, S, Tanaka, N, Nakamura, K.T, Yoshimoto, T.
登録日2004-07-01
公開日2004-07-20
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor
ARCH.BIOCHEM.BIOPHYS., 416, 2003

 

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