5D4I
 
 | | Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, NITRITE ION | | Authors: | Fukuda, Y, Tse, K.M, Nakane, T, Nakatsu, T, Suzuki, M, Sugahara, M, Inoue, S, Masuda, T, Yumoto, F, Matsugaki, N, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Murphy, M.E.P, Inoue, T, Iwata, S, Mizohata, E. | | Deposit date: | 2015-08-07 | | Release date: | 2016-03-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.6 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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2A0B
 | | HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERICHIA COLI | | Descriptor: | HPT DOMAIN, ZINC ION | | Authors: | Kato, M, Mizuno, T, Shimizu, T, Hakoshima, T. | | Deposit date: | 1998-04-02 | | Release date: | 1998-06-17 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Refined structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli at 1.57 A resolution.
Acta Crystallogr.,Sect.D, 55, 1999
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5H9V
 | | Crystal structure of Regnase PIN domain, form I | | Descriptor: | Ribonuclease ZC3H12A, SODIUM ION | | Authors: | Yokogawa, M, Tsushima, T, Adachi, W, Noda, N.N, Inagaki, F. | | Deposit date: | 2015-12-29 | | Release date: | 2016-03-16 | | Last modified: | 2020-02-19 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Sci Rep, 6, 2016
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5H9W
 | | Crystal structure of Regnase PIN domain, form II | | Descriptor: | Ribonuclease ZC3H12A, SODIUM ION | | Authors: | Yokogawa, M, Tsushima, T, Adachi, W, Noda, N.N, Inagaki, F. | | Deposit date: | 2015-12-29 | | Release date: | 2016-03-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Sci Rep, 6, 2016
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1IPD
 | | THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION | | Descriptor: | 3-ISOPROPYLMALATE DEHYDROGENASE, SULFATE ION | | Authors: | Imada, K, Sato, M, Tanaka, N, Katsube, Y, Matsuura, Y, Oshima, T. | | Deposit date: | 1992-01-29 | | Release date: | 1993-10-31 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 A resolution.
J.Mol.Biol., 222, 1991
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1J19
 | | Crystal structure of the radxin FERM domain complexed with the ICAM-2 cytoplasmic peptide | | Descriptor: | 16-mer peptide from Intercellular adhesion molecule-2, radixin | | Authors: | Hamada, K, Shimizu, T, Yonemura, S, Tsukita, S, Tsukita, S, Hakoshima, T. | | Deposit date: | 2002-12-02 | | Release date: | 2003-03-11 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex
EMBO J., 22, 2003
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1UJB
 | | Structure of the protein histidine phosphatase SixA | | Descriptor: | CALCIUM ION, Phosphohistidine phosphatase sixA | | Authors: | Hamada, K, Kato, M, Shimizu, T, Ihara, K, Mizuno, T, Hakoshima, T. | | Deposit date: | 2003-07-31 | | Release date: | 2005-01-25 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Crystal structure of the protein histidine phosphatase SixA in the multistep His-Asp phosphorelay.
Genes Cells, 10, 2005
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1UJC
 | | Structure of the protein histidine phosphatase SixA complexed with tungstate | | Descriptor: | CALCIUM ION, Phosphohistidine phosphatase sixA, TUNGSTATE(VI)ION | | Authors: | Hamada, K, Kato, M, Shimizu, T, Ihara, K, Mizuno, T, Hakoshima, T. | | Deposit date: | 2003-07-31 | | Release date: | 2005-01-25 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of the protein histidine phosphatase SixA in the multistep His-Asp phosphorelay.
Genes Cells, 10, 2005
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1CM7
 | | 3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI | | Descriptor: | PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE) | | Authors: | Wallon, G, Kryger, G, Lovett, S.T, Oshima, T, Ringe, D, Petsko, G.A. | | Deposit date: | 1999-05-17 | | Release date: | 1999-07-01 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus.
J.Mol.Biol., 266, 1997
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6JT4
 | | Crystal Structure of BACE1 in complex with N-{3-[(4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide | | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | | Authors: | Anan, K, Iso, Y, Oguma, T, Nakahara, K, Suzuki, S, Yamamoto, T, Matsuoka, E, Ito, H, Sakaguchi, G, Ando, S, Morimoto, K, Kanegawa, N, Kido, Y, Kawachi, T, Fukushima, T, Teisman, A, Urmaliya, V, Dhuyvetter, D, Borghys, H, Austin, N, Bergh, A.V.D, Verboven, P, Bischoff, F, Gijsen, H.J.M, Yamano, Y, Kusakabe, K.I. | | Deposit date: | 2019-04-08 | | Release date: | 2020-01-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Trifluoromethyl Dihydrothiazine-Based beta-Secretase (BACE1) Inhibitors with Robust Central beta-Amyloid Reduction and Minimal Covalent Binding Burden.
Chemmedchem, 14, 2019
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1CNZ
 | | 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) FROM SALMONELLA TYPHIMURIUM | | Descriptor: | MANGANESE (II) ION, PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE), SULFATE ION | | Authors: | Wallon, G, Kryger, G, Lovett, S.T, Oshima, T, Ringe, D, Petsko, G.A. | | Deposit date: | 1999-05-24 | | Release date: | 1999-06-01 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.76 Å) | | Cite: | Crystal Structures of Eschericia Coli and Salmonella Typhimurium 3-
Isopropylmalate Dehydrogenase and Comparison with Their Thermophilic
Counterpart from Thermus Thermophilus
J.Mol.Biol., 266, 1997
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4YSV
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4YSN
 | | Structure of aminoacid racemase in complex with PLP | | Descriptor: | PYRIDOXAL-5'-PHOSPHATE, Putative 4-aminobutyrate aminotransferase | | Authors: | Sakuraba, H, Mutaguchi, Y, Hayashi, J, Ohshima, T. | | Deposit date: | 2015-03-17 | | Release date: | 2016-04-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.
Acta Crystallogr D Struct Biol, 73, 2017
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7CEE
 | | Crystal structure of mouse neuroligin-3 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Neuroligin-3 | | Authors: | Yamagata, A, Yoshida, T, Shiroshima, T, Maeda, A, Fukai, S. | | Deposit date: | 2020-06-23 | | Release date: | 2021-02-24 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.763 Å) | | Cite: | Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Nat Commun, 12, 2021
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7CEG
 | | Crystal structure of the complex between mouse PTP delta and neuroligin-3 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Isoform C of Receptor-type tyrosine-protein phosphatase delta, Neuroligin-3 | | Authors: | Yamagata, A, Yoshida, T, Shiroshima, T, Maeda, A, Fukai, S. | | Deposit date: | 2020-06-23 | | Release date: | 2021-02-24 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.85 Å) | | Cite: | Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Nat Commun, 12, 2021
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6K3D
 | | Structure of multicopper oxidase mutant | | Descriptor: | COPPER (II) ION, CU-O-CU LINKAGE, Multicopper oxidase | | Authors: | Sakuraba, H, Ohshida, T, Satomura, T, Yoneda, K, Ohshima, T. | | Deposit date: | 2019-05-17 | | Release date: | 2020-05-20 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.919 Å) | | Cite: | Activity enhancement of multicopper oxidase from a hyperthermophile via directed evolution, and its application as the element of a high performance biocathode.
J.Biotechnol., 325, 2021
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7WDT
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S | | Descriptor: | 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose, Beta-N-acetylhexosaminidase, ... | | Authors: | Yamada, C, Kashima, T, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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4ZKF
 | | Crystal structure of human phosphodiesterase 12 | | Descriptor: | 2',5'-phosphodiesterase 12, MAGNESIUM ION | | Authors: | Kim, S.Y, Kohno, T, Mori, T, Kitano, K, Hakoshima, T. | | Deposit date: | 2015-04-30 | | Release date: | 2015-06-17 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Crystal structure of human phosphodiesterase
To Be Published
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2IRF
 | | CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX. | | Descriptor: | DNA (5'-D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3'), DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU)P*GP*A)-3'), INTERFERON REGULATORY FACTOR 2, ... | | Authors: | Fujii, Y, Shimizu, T, Kusumoto, M, Kyogoku, Y, Taniguchi, T, Hakoshima, T. | | Deposit date: | 1999-05-30 | | Release date: | 1999-10-08 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
EMBO J., 18, 1999
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5AUQ
 | | Crystal structure of ATPase-type HypB in the nucleotide free state | | Descriptor: | ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog, ... | | Authors: | Watanabe, S, Kawashima, T, Nishitani, Y, Miki, K. | | Deposit date: | 2015-05-27 | | Release date: | 2015-06-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.525 Å) | | Cite: | Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer
Proc.Natl.Acad.Sci.USA, 112, 2015
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5AUO
 | | Crystal structure of the HypAB-Ni complex (AMPPCP) | | Descriptor: | ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog, ... | | Authors: | Watanabe, S, Kawashima, T, Nishitani, Y, Miki, K. | | Deposit date: | 2015-05-27 | | Release date: | 2015-06-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer
Proc.Natl.Acad.Sci.USA, 112, 2015
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6J9Q
 | | Crystal structure of Trypanosoma brucei gambiense glycerol kinase complex with AMP-PNP. | | Descriptor: | GLYCEROL, Glycerol kinase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Balogun, E.O, Chishima, T, Ichinose, M, Inaoka, D.K, Kido, Y, Ibrahim, B, de Koning, H, McKerrow, J.H, Watanabe, Y, Nozaki, T, Michels, P.A.M, Harada, S, Kita, K, Shiba, T. | | Deposit date: | 2019-01-24 | | Release date: | 2020-01-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Reaction mechanism of the reverse reaction of African human trypanosomes glycerol kinase.
To Be Published
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1XER
 | | STRUCTURE OF FERREDOXIN | | Descriptor: | FE3-S4 CLUSTER, FERREDOXIN, ZINC ION | | Authors: | Fujii, T, Hata, Y, Moriyama, H, Wakagi, T, Tanaka, N, Oshima, T. | | Deposit date: | 1996-08-28 | | Release date: | 1997-09-04 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Novel zinc-binding centre in thermoacidophilic archaeal ferredoxins.
Nat.Struct.Biol., 3, 1996
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8HYE
 | | Structure of amino acid dehydrogenase-2752 with ligand | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Alanine dehydrogenase, ... | | Authors: | Sakuraba, H, Ohshima, T. | | Deposit date: | 2023-01-06 | | Release date: | 2023-04-05 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores.
Biochim Biophys Acta Proteins Proteom, 1871, 2023
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8HYH
 | | Structure of amino acid dehydrogenase3448 | | Descriptor: | 1,2-ETHANEDIOL, Alanine dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Sakuraba, H, Ohshima, T. | | Deposit date: | 2023-01-06 | | Release date: | 2023-04-05 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores.
Biochim Biophys Acta Proteins Proteom, 1871, 2023
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