4YSO
 
 | | Copper nitrite reductase from Geobacillus thermodenitrificans - 0.064 MGy | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, COPPER (II) ION, Nitrite reductase, ... | | Authors: | Fukuda, Y, Tse, K.M, Suzuki, M, Diederichs, K, Hirata, K, Nakane, T, Sugahara, M, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Matsumura, H, Inoue, T, Iwata, S, Mizohata, E. | | Deposit date: | 2015-03-17 | | Release date: | 2016-02-24 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography
J.Biochem., 159, 2016
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2CWH
 | | Crystal Structure of delta1-piperideine-2-carboxylate reductase from Pseudomonas syringae complexed with NADPH and pyrrole-2-carboxylate | | Descriptor: | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PYRROLE-2-CARBOXYLATE, delta1-piperideine-2-carboxylate reductase | | Authors: | Goto, M, Muramatsu, H, Mihara, H, Kurihara, T, Esaki, N, Omi, R, Miyahara, I, Hirotsu, K. | | Deposit date: | 2005-06-20 | | Release date: | 2005-10-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction
J.Biol.Chem., 280, 2005
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2CWF
 | | Crystal Structure of delta1-piperideine-2-carboxylate reductase from Pseudomonas syringae complexed with NADPH | | Descriptor: | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, delta1-piperideine-2-carboxylate reductase | | Authors: | Goto, M, Muramatsu, H, Mihara, H, Kurihara, T, Esaki, N, Omi, R, Miyahara, I, Hirotsu, K. | | Deposit date: | 2005-06-20 | | Release date: | 2005-10-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction
J.Biol.Chem., 280, 2005
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2D0C
 | | Crystal structure of Bst-RNase HIII in complex with Mn2+ | | Descriptor: | MANGANESE (II) ION, ribonuclease HIII | | Authors: | Chon, H, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2005-07-31 | | Release date: | 2006-07-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus
J.Mol.Biol., 356, 2006
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5B1Y
 | | Crystal structure of NADPH bound carbonyl reductase from Aeropyrum pernix | | Descriptor: | 3-oxoacyl-[acyl-carrier-protein] reductase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Yoneda, K, Sakuraba, H, Fukuda, Y, Araki, T, Ohshima, T. | | Deposit date: | 2015-12-22 | | Release date: | 2016-06-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Catalytic properties and crystal structure of thermostable NAD(P)H-dependent carbonyl reductase from the hyperthermophilic archaeon Aeropyrum pernix K1.
Enzyme.Microb.Technol., 91, 2016
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2D0B
 | | Crystal structure of Bst-RNase HIII in complex with Mg2+ | | Descriptor: | MAGNESIUM ION, ribonuclease HIII | | Authors: | Chon, H, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2005-07-31 | | Release date: | 2006-07-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus
J.Mol.Biol., 356, 2006
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2D0A
 | | Crystal structure of Bst-RNase HIII | | Descriptor: | ribonuclease HIII | | Authors: | Chon, H, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2005-07-31 | | Release date: | 2006-07-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus
J.Mol.Biol., 356, 2006
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3W82
 | | Human alpha-L-iduronidase in complex with iduronic acid | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Alpha-L-iduronidase, ... | | Authors: | Maita, N, Tsukimura, T, Taniguchi, T, Saito, S, Ohno, K, Taniguchi, H, Sakuraba, H. | | Deposit date: | 2013-03-11 | | Release date: | 2013-08-21 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.76 Å) | | Cite: | Human alpha-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module
Proc.Natl.Acad.Sci.USA, 110, 2013
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3W81
 | | Human alpha-l-iduronidase | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Alpha-L-iduronidase, ... | | Authors: | Maita, N, Tsukimura, T, Taniguchi, T, Saito, S, Ohno, K, Taniguchi, H, Sakuraba, H. | | Deposit date: | 2013-03-11 | | Release date: | 2013-08-21 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Human alpha-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WA9
 | | The nucleosome containing human H2A.Z.1 | | Descriptor: | DNA (146-MER), Histone H2A.Z, Histone H2B type 1-J, ... | | Authors: | Horikoshi, N, Sato, K, Shimada, K, Arimura, Y, Osakabe, A, Tachiwana, H, Iwasaki, W, Kagawa, W, Harata, M, Kimura, H, Kurumizaka, H. | | Deposit date: | 2013-04-30 | | Release date: | 2013-12-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.07 Å) | | Cite: | Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
Acta Crystallogr.,Sect.D, 69, 2013
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3WAA
 | | The nucleosome containing human H2A.Z.2 | | Descriptor: | DNA (146-MER), Histone H2A.V, Histone H2B type 1-J, ... | | Authors: | Horikoshi, N, Sato, K, Shimada, K, Arimura, Y, Osakabe, A, Tachiwana, H, Iwasaki, W, Kagawa, W, Harata, M, Kimura, H, Kurumizaka, H. | | Deposit date: | 2013-04-30 | | Release date: | 2013-12-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
Acta Crystallogr.,Sect.D, 69, 2013
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2E5V
 | | Crystal structure of L-Aspartate Oxidase from hyperthermophilic archaeon Sulfolobus tokodaii | | Descriptor: | CHLORIDE ION, FLAVIN-ADENINE DINUCLEOTIDE, L-aspartate oxidase | | Authors: | Yoneda, K, Sakuraba, H, Asai, I, Tsuge, H, Katunuma, N, Ohshima, T. | | Deposit date: | 2006-12-25 | | Release date: | 2008-01-01 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Structure of l-aspartate oxidase from the hyperthermophilic archaeon Sulfolobus tokodaii
Biochim.Biophys.Acta, 1784, 2008
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2E4L
 | | Thermodynamic and Structural Analysis of Thermolabile RNase HI from Shewanella oneidensis MR-1 | | Descriptor: | Ribonuclease HI | | Authors: | Tadokoro, T, You, D.J, Chon, H, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2006-12-13 | | Release date: | 2007-05-01 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI.
Biochemistry, 46, 2007
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1GZA
 | | PEROXIDASE | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, IODIDE ION, ... | | Authors: | Fukuyama, K, Itakura, H. | | Deposit date: | 1996-11-13 | | Release date: | 1997-03-12 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Binding of iodide to Arthromyces ramosus peroxidase investigated with X-ray crystallographic analysis, 1H and 127I NMR spectroscopy, and steady-state kinetics.
J.Biol.Chem., 272, 1997
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3X2S
 | | Crystal structure of pyrene-conjugated adenylate kinase | | Descriptor: | Adenylate kinase, BIS(ADENOSINE)-5'-PENTAPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Fujii, A, Sekiguchi, Y, Matsumura, H, Inoue, T, Chung, W.-S, Hirota, S, Matsuo, T. | | Deposit date: | 2014-12-31 | | Release date: | 2015-04-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Excimer Emission Properties on Pyrene-Labeled Protein Surface: Correlation between Emission Spectra, Ring Stacking Modes, and Flexibilities of Pyrene Probes.
Bioconjug.Chem., 26, 2015
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2E1P
 | | Crystal structure of pro-Tk-subtilisin | | Descriptor: | CALCIUM ION, Tk-subtilisin | | Authors: | Tanaka, S, Saito, K, Chon, H, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2006-10-27 | | Release date: | 2007-01-16 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of unautoprocessed precursor of subtilisin from a hyperthermophilic archaeon: evidence for Ca2+-induced folding
J.Biol.Chem., 282, 2007
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5YCJ
 | | Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) imidazole-ligand | | Descriptor: | Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly), IMIDAZOLE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Isogai, Y, Imamura, H, Nakae, S, Sumi, T, Takahashi, K, Nakagawa, T, Tsuneshige, A, Shirai, T. | | Deposit date: | 2017-09-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Tracing whale myoglobin evolution by resurrecting ancient proteins.
Sci Rep, 8, 2018
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1IR1
 | | Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, Large subunit of Rubisco, MAGNESIUM ION, ... | | Authors: | Mizohata, E, Matsumura, H, Okano, Y, Kumei, M, Takuma, H, Onodera, J, Kato, K, Shibata, N, Inoue, T, Yokota, A, Kai, Y. | | Deposit date: | 2001-08-31 | | Release date: | 2002-03-13 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
J.Mol.Biol., 316, 2002
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8HTB
 | | Staphylococcus aureus FtsZ 12-316 complexed with TXH9179 | | Descriptor: | 3-[(6-ethynyl-[1,3]thiazolo[5,4-b]pyridin-2-yl)methoxy]-2,6-bis(fluoranyl)benzamide, CALCIUM ION, Cell division protein FtsZ, ... | | Authors: | Bryan, E, Ferrer-Gonzalez, E, Sagong, H.Y, Fujita, J, Mark, L, Kaul, M, LaVoie, E.J, Matsumura, H, Pilch, D.S. | | Deposit date: | 2022-12-21 | | Release date: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Structural and Antibacterial Characterization of a New Benzamide FtsZ Inhibitor with Superior Bactericidal Activity and In Vivo Efficacy Against Multidrug-Resistant Staphylococcus aureus.
Acs Chem.Biol., 18, 2023
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1HR9
 | | Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, MALATE DEHYDROGENASE, MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, ... | | Authors: | Taylor, A.B, Smith, B.S, Kitada, S, Kojima, K, Miyaura, H, Otwinowski, Z, Ito, A, Deisenhofer, J. | | Deposit date: | 2000-12-21 | | Release date: | 2001-07-11 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (3.01 Å) | | Cite: | Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.
Structure, 9, 2001
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1HSR
 | | BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BENZHYDROXAMIC ACID, CALCIUM ION, ... | | Authors: | Fukuyama, K, Itakura, H. | | Deposit date: | 1997-07-01 | | Release date: | 1998-07-01 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution.
FEBS Lett., 412, 1997
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4YSC
 | | Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis | | Descriptor: | CHLORIDE ION, COPPER (II) ION, Copper-containing nitrite reductase | | Authors: | Fukuda, Y, Tse, K.M, Suzuki, M, Diederichs, K, Hirata, K, Nakane, T, Sugahara, M, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Matsumura, H, Inoue, T, Iwata, S, Mizohata, E. | | Deposit date: | 2015-03-17 | | Release date: | 2016-03-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Proc.Natl.Acad.Sci.USA, 113, 2016
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4YSE
 | | High resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, ACETIC ACID, COPPER (II) ION, ... | | Authors: | Fukuda, Y, Tse, K.M, Suzuki, M, Diederichs, K, Hirata, K, Nakane, T, Sugahara, M, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Matsumura, H, Inoue, T, Iwata, S, Mizohata, E. | | Deposit date: | 2015-03-17 | | Release date: | 2016-03-09 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Proc.Natl.Acad.Sci.USA, 113, 2016
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1HR7
 | | Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant | | Descriptor: | MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, ZINC ION | | Authors: | Taylor, A.B, Smith, B.S, Kitada, S, Kojima, K, Miyaura, H, Otwinowski, Z, Ito, A, Deisenhofer, J. | | Deposit date: | 2000-12-21 | | Release date: | 2001-07-11 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.
Structure, 9, 2001
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8IMR
 | | Structure of ligand-free human macrophage migration inhibitory factor | | Descriptor: | 1,2-ETHANEDIOL, ISOPROPYL ALCOHOL, Macrophage migration inhibitory factor, ... | | Authors: | Sugishima, K, Noguchi, K, Yohda, M, Odaka, M, Matsumura, H. | | Deposit date: | 2023-03-07 | | Release date: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Identification of methotrexate as an inhibitor of macrophage migration inhibitory factor by high-resolution crystal structure analysis
To Be Published
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