4UB8
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![BU of 4ub8 by Molmil](/molmil-images/mine/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: | 2024-03-20 | 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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4UB6
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![BU of 4ub6 by Molmil](/molmil-images/mine/4ub6) | Native structure of photosystem II (dataset-1) 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: | 2024-03-20 | 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
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![BU of 8wey by Molmil](/molmil-images/mine/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: | 2024-03-13 | 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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8GN2
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![BU of 8gn2 by Molmil](/molmil-images/mine/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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8GN0
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![BU of 8gn0 by Molmil](/molmil-images/mine/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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8GN1
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![BU of 8gn1 by Molmil](/molmil-images/mine/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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1V7Z
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![BU of 1v7z by Molmil](/molmil-images/mine/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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1UDY
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![BU of 1udy by Molmil](/molmil-images/mine/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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7D1T
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![BU of 7d1t by Molmil](/molmil-images/mine/7d1t) | Cryo-EM Structure of PSII at 1.95 angstrom resolution | 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: | Kato, K, Miyazaki, N, Hamaguchi, T, Nakajima, Y, Akita, F, Yonekura, K, Shen, J.R. | Deposit date: | 2020-09-15 | Release date: | 2021-03-31 | Last modified: | 2021-04-07 | Method: | ELECTRON MICROSCOPY (1.95 Å) | Cite: | High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. Commun Biol, 4, 2021
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7D1U
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![BU of 7d1u by Molmil](/molmil-images/mine/7d1u) | Cryo-EM Structure of PSII at 2.08 angstrom resolution | 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: | Kato, K, Miyazaki, N, Hamaguchi, T, Nakajima, Y, Akita, F, Yonekura, K, Shen, J.R. | Deposit date: | 2020-09-15 | Release date: | 2021-03-31 | Last modified: | 2021-04-07 | Method: | ELECTRON MICROSCOPY (2.08 Å) | Cite: | High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. Commun Biol, 4, 2021
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1ULZ
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![BU of 1ulz by Molmil](/molmil-images/mine/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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7EDA
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![BU of 7eda by Molmil](/molmil-images/mine/7eda) | Structure of monomeric photosystem II | 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: | Yu, H, Hamaguchi, T, Nakajima, Y, Kato, K, kawakami, K, Akita, F, Yonekura, K, Shen, J.R. | Deposit date: | 2021-03-15 | Release date: | 2021-07-07 | Last modified: | 2021-08-04 | Method: | ELECTRON MICROSCOPY (2.78 Å) | Cite: | Cryo-EM structure of monomeric photosystem II at 2.78 angstrom resolution reveals factors important for the formation of dimer. Biochim Biophys Acta Bioenerg, 1862, 2021
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1J2T
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![BU of 1j2t by Molmil](/molmil-images/mine/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
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![BU of 1j2u by Molmil](/molmil-images/mine/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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2DQM
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![BU of 2dqm by Molmil](/molmil-images/mine/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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2DDH
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![BU of 2ddh by Molmil](/molmil-images/mine/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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2EEP
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![BU of 2eep by Molmil](/molmil-images/mine/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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2Z3Z
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![BU of 2z3z by Molmil](/molmil-images/mine/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: | 2023-11-01 | 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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1IX6
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![BU of 1ix6 by Molmil](/molmil-images/mine/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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1X1T
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![BU of 1x1t by Molmil](/molmil-images/mine/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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2Z3W
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![BU of 2z3w by Molmil](/molmil-images/mine/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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1IX8
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![BU of 1ix8 by Molmil](/molmil-images/mine/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
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![BU of 1ix7 by Molmil](/molmil-images/mine/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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![BU of 1kh2 by Molmil](/molmil-images/mine/1kh2) | |
1KH1
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![BU of 1kh1 by Molmil](/molmil-images/mine/1kh1) | |