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1IS2
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BU of 1is2 by Molmil
Crystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver
Descriptor: FLAVIN-ADENINE DINUCLEOTIDE, acyl-CoA oxidase
Authors:Nakajima, Y, Miyahara, I, Hirotsu, K.
Deposit date:2001-11-07
Release date:2002-04-10
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite: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
1X2E
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BU of 1x2e by Molmil
The crystal structure of prolyl aminopeptidase complexed with Ala-TBODA
Descriptor: (2S)-2-AMINO-1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)PROPAN-1-ONE, Proline iminopeptidase
Authors:Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T.
Deposit date:2005-04-22
Release date:2006-05-09
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.4 Å)
Cite: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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BU of 1x2b by Molmil
The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA
Descriptor: 1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-2-(METHYLAMINO)ETHANONE, Proline iminopeptidase
Authors:Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T.
Deposit date:2005-04-22
Release date:2006-05-09
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
J.Bacteriol., 188, 2006
1V93
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BU of 1v93 by Molmil
5,10-Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8
Descriptor: 1,4-DIETHYLENE DIOXIDE, 5,10-Methylenetetrahydrofolate reductase, FLAVIN-ADENINE DINUCLEOTIDE
Authors:Nakajima, Y, Miyahara, I, Hirotsu, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-20
Release date:2004-02-03
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal Structure of 5,10-Methylenetetrahydrofolate reductase from Thermus thermophilus HB8
To be Published
5ZZN
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BU of 5zzn by Molmil
Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus
Descriptor: (3R)-beta,beta-caroten-3-ol, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ...
Authors:Nakajima, Y, Umena, Y, Nagao, R, Endo, K, Kobayashi, K, Akita, F, Suga, M, Wada, H, Noguchi, T, Shen, J.R.
Deposit date:2018-06-03
Release date:2018-08-01
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.
J. Biol. Chem., 293, 2018
2ECF
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BU of 2ecf by Molmil
Crystal Structure of Dipeptidyl Aminopeptidase IV from Stenotrophomonas maltophilia
Descriptor: Dipeptidyl peptidase IV
Authors:Nakajima, Y, Ito, K, Yoshimoto, T.
Deposit date:2007-02-13
Release date:2008-02-26
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue
J.Bacteriol., 190, 2008
7VKD
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BU of 7vkd by Molmil
Reduced enzyme of FAD-dpendent Glucose Dehydrogenase at pH6.5
Descriptor: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE, GMC oxidoreductase
Authors:Nakajima, Y, Nishiya, Y, Ito, K.
Deposit date:2021-09-29
Release date:2022-10-05
Last modified:2022-10-12
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
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
Descriptor: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, D-glucono-1,5-lactone, DIHYDROFLAVINE-ADENINE DINUCLEOTIDE, ...
Authors:Nakajima, Y, Nishiya, Y, Ito, K.
Deposit date:2021-09-29
Release date:2022-10-05
Last modified:2022-10-12
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
7VZS
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BU of 7vzs by Molmil
FAD-dpendent Glucose Dehydrogenase complexed with an inhibitor at pH7.56
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, D-glucal, FLAVIN-ADENINE DINUCLEOTIDE, ...
Authors:Nakajima, Y.
Deposit date:2021-11-16
Release date:2022-11-16
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
7VZP
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BU of 7vzp by Molmil
FAD-dpendent Glucose Dehydrogenase from Aspergillus oryzae
Descriptor: FLAVIN-ADENINE DINUCLEOTIDE, GMC oxidoreductase, PENTAETHYLENE GLYCOL
Authors:Nakajima, Y.
Deposit date:2021-11-16
Release date:2022-11-16
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
To Be Published
7YQ2
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BU of 7yq2 by Molmil
Crystal structure of photosystem II expressing psbA2 gene only
Descriptor: (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, ...
Authors:Nakajima, Y, Suga, M, Shen, J.R.
Deposit date:2022-08-05
Release date:2022-11-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite: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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BU of 7yq7 by Molmil
Crystal structure of photosystem II expressing psbA3 gene only
Descriptor: (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, ...
Authors:Nakajima, Y, Suga, M, Shen, J.R.
Deposit date:2022-08-05
Release date:2022-11-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite: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
2D5L
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BU of 2d5l by Molmil
Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
Descriptor: SULFATE ION, dipeptidyl aminopeptidase IV, putative
Authors:Nakajima, Y, Ito, K, Xu, Y, Yamada, N, Onohara, Y, Yoshimoto, T.
Deposit date:2005-11-02
Release date:2006-09-19
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal Structure and Mechanism of Tripeptidyl Activity of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
J.Mol.Biol., 362, 2006
2DCM
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BU of 2dcm by Molmil
The Crystal Structure of S603A Mutated Prolyl Tripeptidyl Aminopeptidase Complexed with Substrate
Descriptor: GLYCYLALANYL-N-2-NAPHTHYL-L-PROLINEAMIDE, dipeptidyl aminopeptidase IV, putative
Authors:Nakajima, Y, Ito, K, Xu, Y, Yamada, N, Onohara, Y, Yoshimoto, T.
Deposit date:2006-01-09
Release date:2006-09-19
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Crystal Structure and Mechanism of Tripeptidyl Activity of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
J.Mol.Biol., 362, 2006
2DQ6
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BU of 2dq6 by Molmil
Crystal Structure of Aminopeptidase N from Escherichia coli
Descriptor: Aminopeptidase N, SULFATE ION, ZINC ION
Authors:Nakajima, Y, Onohara, Y, Ito, K, Yoshimoto, T.
Deposit date:2006-05-22
Release date:2006-08-01
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite: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
3A6J
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BU of 3a6j by Molmil
E122Q mutant creatininase complexed with creatine
Descriptor: Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite: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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BU of 3a6d by Molmil
Creatininase complexed with 1-methylguanidine
Descriptor: 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.9 Å)
Cite: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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BU of 3a6f by Molmil
W174F mutant creatininase, Type II
Descriptor: CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.78 Å)
Cite: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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BU of 3a6g by Molmil
W154F mutant creatininase
Descriptor: Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite: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
3A6E
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BU of 3a6e by Molmil
W174F mutant creatininase, type I
Descriptor: CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite: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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BU of 3a6k by Molmil
The E122Q mutant creatininase, Mn-Zn type
Descriptor: CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite: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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BU of 3a6h by Molmil
W154A mutant creatininase
Descriptor: CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite: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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BU of 3a6l by Molmil
E122Q mutant creatininase, Zn-Zn type
Descriptor: CHLORIDE ION, Creatinine amidohydrolase, ZINC ION
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite: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
2ZXG
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BU of 2zxg by Molmil
Aminopeptidase N complexed with the aminophosphinic inhibitor of PL250, a transition state analogue
Descriptor: Aminopeptidase N, GLYCEROL, N-{(2S)-3-[(1R)-1-aminoethyl](hydroxy)phosphoryl-2-benzylpropanoyl}-L-phenylalanine, ...
Authors:Nakajima, Y, Ito, K, Yoshimoto, T.
Deposit date:2008-12-24
Release date:2009-08-25
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Structure of aminopeptidase N from Escherichia coli complexed with the transition-state analogue aminophosphinic inhibitor PL250
Acta Crystallogr.,Sect.D, 65, 2009
4UB8
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BU of 4ub8 by Molmil
Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser
Descriptor: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ...
Authors:Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R.
Deposit date:2014-08-12
Release date:2014-12-03
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015

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