4UB8
 
 | | 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: | 2024-10-23 | | 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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8WEY
 | | PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137) | | Descriptor: | (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, BETA-CAROTENE, ... | | Authors: | Kato, K, Hamaguchi, T, Nakajima, Y, Kawakami, K, Yonekura, K, Shen, J.R, Nagao, R. | | Deposit date: | 2023-09-19 | | Release date: | 2024-02-14 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (1.92 Å) | | Cite: | The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.
Proc.Natl.Acad.Sci.USA, 121, 2024
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8XLS
 | | PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335 | | Descriptor: | (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol, (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate, ... | | Authors: | Kato, K, Nakajima, Y, Shen, J.R, Nagao, R. | | Deposit date: | 2023-12-26 | | Release date: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex
Elife, 2024
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1UDY
 | | Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA | | Descriptor: | 3-THIAOCTANOYL-COENZYME A, Acyl-CoA dehydrogenase, medium-chain specific, ... | | Authors: | Satoh, A, Nakajima, Y, Miyahara, I, Hirotsu, K, Tanaka, T, Nishina, Y, Shiga, K, Tamaoki, H, Setoyama, C, Miura, R. | | Deposit date: | 2003-05-07 | | Release date: | 2003-12-09 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
J.BIOCHEM.(TOKYO), 134, 2003
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1V7Z
 | | creatininase-product complex | | Descriptor: | MANGANESE (II) ION, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ... | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-12-26 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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1J2T
 | | Creatininase Mn | | Descriptor: | MANGANESE (II) ION, SULFATE ION, ZINC ION, ... | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-01-11 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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1J2U
 | | Creatininase Zn | | Descriptor: | SULFATE ION, ZINC ION, creatinine amidohydrolase | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-01-11 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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1ULZ
 | | Crystal structure of the biotin carboxylase subunit of pyruvate carboxylase | | Descriptor: | pyruvate carboxylase n-terminal domain | | Authors: | Kondo, S, Nakajima, Y, Sugio, S, Yong-Biao, J, Sueda, S, Kondo, H. | | Deposit date: | 2003-09-18 | | Release date: | 2004-03-09 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structure of the biotin carboxylase subunit of pyruvate carboxylase from Aquifex aeolicus at 2.2 A resolution.
Acta Crystallogr.,Sect.D, 60, 2004
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8GN0
 | | Crystal structure of DCBQ-bound photosystem II complex | | 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: | Kamada, S, Nakajima, Y, Shen, J.-R. | | Deposit date: | 2022-08-22 | | Release date: | 2023-07-05 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.
J.Biol.Chem., 299, 2023
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8GN2
 | | Crystal structure of PPBQ-bound photosystem II complex | | 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: | Kamada, S, Nakajima, Y, Shen, J.-R. | | Deposit date: | 2022-08-22 | | Release date: | 2023-07-05 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.
J.Biol.Chem., 299, 2023
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8GN1
 | | Crystal structure of DBBQ-bound photosystem II complex | | 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: | Kamada, S, Nakajima, Y, Shen, J.-R. | | Deposit date: | 2022-08-22 | | Release date: | 2023-07-05 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.
J.Biol.Chem., 299, 2023
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2DQM
 | | Crystal Structure of Aminopeptidase N complexed with bestatin | | Descriptor: | 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID, Aminopeptidase N, SULFATE ION, ... | | Authors: | Onohara, Y, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2006-05-29 | | Release date: | 2006-08-01 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 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
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2EEP
 | | Prolyl Tripeptidyl Aminopeptidase Complexed with an Inhibitor | | Descriptor: | Dipeptidyl aminopeptidase IV, putative, SULFATE ION, ... | | Authors: | Xu, Y, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2007-02-16 | | Release date: | 2008-02-19 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism
J.Mol.Biol., 375, 2008
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2DDH
 | | Crystal Structure of Acyl-CoA oxidase complexed with 3-OH-dodecanoate | | Descriptor: | (3R)-3-HYDROXYDODECANOIC ACID, Acyl-CoA oxidase, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Keiji, T, Nakajima, Y, Miyahara, I, Hirotsu, K. | | Deposit date: | 2006-01-29 | | Release date: | 2006-03-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Three-Dimensional Structure of Rat-Liver Acyl-CoA Oxidase in Complex with a Fatty Acid: Insights into Substrate-Recognition and Reactivity toward Molecular Oxygen.
J.Biochem.(Tokyo), 139, 2006
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1IX8
 | | Aspartate Aminotransferase Active Site Mutant V39F/N194A | | Descriptor: | Aspartate Aminotransferase, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Hayashi, H, Mizuguchi, H, Miyahara, I, Nakajima, Y, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 2002-06-14 | | Release date: | 2002-07-03 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
J.BIOL.CHEM., 278, 2003
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1IX7
 | | Aspartate Aminotransferase Active Site Mutant V39F maleate complex | | Descriptor: | Aspartate Aminotransferase, MALEIC ACID, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Hayashi, H, Mizuguchi, H, Miyahara, I, Nakajima, Y, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 2002-06-14 | | Release date: | 2002-07-03 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
J.BIOL.CHEM., 278, 2003
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1KH2
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1KOR
 | | Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitors | | Descriptor: | ARGININE, Argininosuccinate Synthetase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | | Authors: | Goto, M, Nakajima, Y, Hirotsu, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-12-22 | | Release date: | 2002-04-03 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action.
J.Biol.Chem., 277, 2002
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1IX6
 | | Aspartate Aminotransferase Active Site Mutant V39F | | Descriptor: | Aspartate Aminotransferase, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Hayashi, H, Mizuguchi, H, Miyahara, I, Nakajima, Y, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 2002-06-14 | | Release date: | 2002-07-03 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
J.BIOL.CHEM., 278, 2003
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1KH1
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2Z3W
 | | Prolyl tripeptidyl aminopeptidase mutant E636A | | Descriptor: | Dipeptidyl aminopeptidase IV, GLYCEROL, SULFATE ION | | Authors: | Xu, Y, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2007-06-07 | | Release date: | 2008-02-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism
J.Mol.Biol., 375, 2008
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2Z3Z
 | | Prolyl tripeptidyl aminopeptidase mutant E636A complexd with an inhibitor | | Descriptor: | Dipeptidyl aminopeptidase IV, SULFATE ION, [(2R)-1-(L-ALANYL-L-ISOLEUCYL)PYRROLIDIN-2-YL]BORONIC ACID | | Authors: | Xu, Y, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2007-06-09 | | Release date: | 2008-02-19 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism
J.Mol.Biol., 375, 2008
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1WMB
 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase | | Descriptor: | CACODYLATE ION, D(-)-3-hydroxybutyrate dehydrogenase, MAGNESIUM ION | | Authors: | Ito, K, Nakajima, Y, Ichihara, E, Ogawa, K, Yoshimoto, T. | | Deposit date: | 2004-07-06 | | Release date: | 2005-09-06 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | d-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi: Molecular Cloning of the Enzyme Gene and Crystal Structure of the Enzyme
J.Mol.Biol., 355, 2006
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1X3X
 | | Crystal Structure of Cytochrome b5 from Ascaris suum | | Descriptor: | Cytochrome b5, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION | | Authors: | Yokota, T, Nakajima, Y, Yamakura, F, Sugio, S, Hashimoto, M, Takamiya, S, Aoki, T. | | Deposit date: | 2005-05-11 | | Release date: | 2006-06-06 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Unique structure of Ascaris suum b5-type cytochrome: an additional alpha-helix and positively charged residues on the surface domain interact with redox partners
Biochem.J., 394, 2006
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1X1T
 | | Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+ | | Descriptor: | CACODYLATE ION, D(-)-3-hydroxybutyrate dehydrogenase, MAGNESIUM ION, ... | | Authors: | Ito, K, Nakajima, Y, Ichihara, E, Ogawa, K, Yoshimoto, T. | | Deposit date: | 2005-04-13 | | Release date: | 2006-01-10 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | d-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi: Molecular Cloning of the Enzyme Gene and Crystal Structure of the Enzyme
J.Mol.Biol., 355, 2006
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