5X7B
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![BU of 5x7b by Molmil](/molmil-images/mine/5x7b) | Crystal structure of SHP2_SH2-CagA EPIYA_C peptide complex | Descriptor: | CagA, Tyrosine-protein phosphatase non-receptor type 11 | Authors: | Senda, M, Senda, T. | Deposit date: | 2017-02-24 | Release date: | 2017-09-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Differential Mechanisms for SHP2 Binding and Activation Are Exploited by Geographically Distinct Helicobacter pylori CagA Oncoproteins. Cell Rep, 20, 2017
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4DVY
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![BU of 4dvy by Molmil](/molmil-images/mine/4dvy) | Crystal structure of the Helicobacter pylori CagA oncoprotein | Descriptor: | Cytotoxicity-associated immunodominant antigen | Authors: | Hayashi, T, Senda, M, Morohashi, H, Higashi, H, Horio, M, Kashiba, Y, Nagase, L, Sasaya, D, Shimizu, T, Venugopalan, N, Kumeta, H, Noda, N, Inagaki, F, Senda, T, Hatakeyama, M. | Deposit date: | 2012-02-23 | Release date: | 2012-07-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Tertiary Structure-Function Analysis Reveals the Pathogenic Signaling Potentiation Mechanism of Helicobacter pylori Oncogenic Effector CagA Cell Host Microbe, 12, 2012
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4DVZ
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![BU of 4dvz by Molmil](/molmil-images/mine/4dvz) | Crystal structure of the Helicobacter pylori CagA oncoprotein | Descriptor: | Cytotoxicity-associated immunodominant antigen | Authors: | Hayashi, T, Senda, M, Morohashi, H, Higashi, H, Horio, M, Kashiba, Y, Nagase, L, Sasaya, D, Shimizu, T, Venugopalan, N, Kumeta, H, Noda, N, Inagaki, F, Senda, T, Hatakeyama, M. | Deposit date: | 2012-02-23 | Release date: | 2012-07-25 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3.19 Å) | Cite: | Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA Cell Host Microbe, 12, 2012
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8Y6H
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![BU of 8y6h by Molmil](/molmil-images/mine/8y6h) | P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in LMNG detergent | Descriptor: | ATP-dependent translocase ABCB1,mNeonGreen, UIC2 Fab heavy chain, UIC2 Fab light chain, ... | Authors: | Hamaguchi-Suzuki, N, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Anzai, N, Senda, T, Murata, T. | Deposit date: | 2024-02-02 | Release date: | 2024-04-17 | Method: | ELECTRON MICROSCOPY (2.49 Å) | Cite: | Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Biochem.Biophys.Res.Commun., 709, 2024
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8Y6I
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![BU of 8y6i by Molmil](/molmil-images/mine/8y6i) | P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in nanodisc | Descriptor: | 1,2-Distearoyl-sn-glycerophosphoethanolamine, ATP-dependent translocase ABCB1,mNeonGreen, CHOLESTEROL, ... | Authors: | Hamaguchi-Suzuki, N, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Anzai, N, Senda, T, Murata, T. | Deposit date: | 2024-02-02 | Release date: | 2024-04-17 | Method: | ELECTRON MICROSCOPY (2.54 Å) | Cite: | Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Biochem.Biophys.Res.Commun., 709, 2024
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2V9Z
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![BU of 2v9z by Molmil](/molmil-images/mine/2v9z) | Structure of the Rhodococcus haloalkane dehalogenase mutant with enhanced enantioselectivity | Descriptor: | HALOALKANE DEHALOGENASE | Authors: | Koudelakova, T, Prokop, Z, Sato, Y, Lapkouski, M, Chovancova, E, Monincova, M, Jesenska, A, Emmer, J, Senda, T, Nagata, Y, Kuta Smatanova, I, Damborsky, J. | Deposit date: | 2007-08-28 | Release date: | 2008-09-16 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Rational Engineering of Rhodococcus Haloalkane Dehalogenase with Enhanced Enantioselectivity To be Published
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5XL0
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![BU of 5xl0 by Molmil](/molmil-images/mine/5xl0) | met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a heme possesseing CF3 group as side chain | Descriptor: | Myoglobin, SULFATE ION, fluorinated heme | Authors: | Kanai, Y, Harada, A, Shibata, T, Nishimura, R, Namiki, K, Watanabe, M, Nakamura, S, Yumoto, F, Senda, T, Suzuki, A, Neya, S, Yamamoto, Y. | Deposit date: | 2017-05-10 | Release date: | 2017-08-16 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor Biochemistry, 56, 2017
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2E4Q
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![BU of 2e4q by Molmil](/molmil-images/mine/2e4q) | Crystal structure of BphA3 (reduced form) | Descriptor: | Biphenyl dioxygenase ferredoxin subunit, FE2/S2 (INORGANIC) CLUSTER | Authors: | Senda, M, Kishigami, S, Kimura, S, Ishida, T, Fukuda, M, Senda, T. | Deposit date: | 2006-12-15 | Release date: | 2007-10-16 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin J.Mol.Biol., 373, 2007
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2E50
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![BU of 2e50 by Molmil](/molmil-images/mine/2e50) | Crystal structure of SET/TAF-1beta/INHAT | Descriptor: | Protein SET, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose | Authors: | Muto, S, Senda, M, Senda, T, Horikoshi, M. | Deposit date: | 2006-12-18 | Release date: | 2007-02-20 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity Proc.Natl.Acad.Sci.Usa, 104, 2007
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2E4P
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![BU of 2e4p by Molmil](/molmil-images/mine/2e4p) | Crystal structure of BphA3 (oxidized form) | Descriptor: | Biphenyl dioxygenase ferredoxin subunit, FE2/S2 (INORGANIC) CLUSTER, SULFATE ION, ... | Authors: | Senda, M, Kishigami, S, Kimura, S, Ishida, T, Fukuda, M, Senda, T. | Deposit date: | 2006-12-15 | Release date: | 2007-10-16 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin J.Mol.Biol., 373, 2007
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5X1L
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![BU of 5x1l by Molmil](/molmil-images/mine/5x1l) | Vanillate/3-O-methylgallate O-demethylase, LigM, tetrahydrofolate complex form | Descriptor: | (6S)-5,6,7,8-TETRAHYDROFOLATE, 1,2-ETHANEDIOL, Vanillate/3-O-methylgallate O-demethylase | Authors: | Harada, A, Senda, T. | Deposit date: | 2017-01-26 | Release date: | 2017-05-17 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6 FEBS J., 284, 2017
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4GNC
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![BU of 4gnc by Molmil](/molmil-images/mine/4gnc) | human SMP30/GNL-1,5-AG complex | Descriptor: | 1,5-anhydro-D-glucitol, CALCIUM ION, Regucalcin | Authors: | Aizawa, S, Senda, M, Harada, A, Maruyama, N, Ishida, T, Aigaki, T, Ishigami, A, Senda, T. | Deposit date: | 2012-08-17 | Release date: | 2013-04-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.749 Å) | Cite: | Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase Plos One, 8, 2013
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4GNA
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![BU of 4gna by Molmil](/molmil-images/mine/4gna) | mouse SMP30/GNL-xylitol complex | Descriptor: | CALCIUM ION, Regucalcin, SULFATE ION, ... | Authors: | Aizawa, S, Senda, M, Harada, A, Maruyama, N, Ishida, T, Aigaki, T, Ishigami, A, Senda, T. | Deposit date: | 2012-08-17 | Release date: | 2013-04-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase Plos One, 8, 2013
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4GNB
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![BU of 4gnb by Molmil](/molmil-images/mine/4gnb) | human SMP30/GNL | Descriptor: | CALCIUM ION, Regucalcin | Authors: | Aizawa, S, Senda, M, Harada, A, Maruyama, N, Ishida, T, Aigaki, T, Ishigami, A, Senda, T. | Deposit date: | 2012-08-17 | Release date: | 2013-04-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase Plos One, 8, 2013
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4GN7
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![BU of 4gn7 by Molmil](/molmil-images/mine/4gn7) | mouse SMP30/GNL | Descriptor: | CALCIUM ION, Regucalcin, SULFATE ION | Authors: | Aizawa, S, Senda, M, Harada, A, Maruyama, N, Ishida, T, Aigaki, T, Ishigami, A, Senda, T. | Deposit date: | 2012-08-17 | Release date: | 2013-04-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase Plos One, 8, 2013
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4GN8
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![BU of 4gn8 by Molmil](/molmil-images/mine/4gn8) | mouse SMP30/GNL-1,5-AG complex | Descriptor: | 1,5-anhydro-D-glucitol, CALCIUM ION, Regucalcin, ... | Authors: | Aizawa, S, Senda, M, Harada, A, Maruyama, N, Ishida, T, Aigaki, T, Ishigami, A, Senda, T. | Deposit date: | 2012-08-17 | Release date: | 2013-04-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase Plos One, 8, 2013
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4GN9
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![BU of 4gn9 by Molmil](/molmil-images/mine/4gn9) | mouse SMP30/GNL-glucose complex | Descriptor: | CALCIUM ION, Regucalcin, SULFATE ION, ... | Authors: | Aizawa, S, Senda, M, Harada, A, Maruyama, N, Ishida, T, Aigaki, T, Ishigami, A, Senda, T. | Deposit date: | 2012-08-17 | Release date: | 2013-04-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase Plos One, 8, 2013
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1ULI
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![BU of 1uli by Molmil](/molmil-images/mine/1uli) | Biphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strain RHA1 | Descriptor: | FE (II) ION, FE2/S2 (INORGANIC) CLUSTER, biphenyl dioxygenase large subunit, ... | Authors: | Furusawa, Y, Nagarajan, V, Masai, E, Tanokura, M, Fukuda, M, Senda, T. | Deposit date: | 2003-09-12 | Release date: | 2004-09-28 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1 J.Mol.Biol., 342, 2004
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1ULJ
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![BU of 1ulj by Molmil](/molmil-images/mine/1ulj) | Biphenyl dioxygenase (BphA1A2) in complex with the substrate | Descriptor: | BIPHENYL, FE (II) ION, FE2/S2 (INORGANIC) CLUSTER, ... | Authors: | Furusawa, Y, Nagarajan, V, Masai, E, Tanokura, M, Fukuda, M, Senda, T. | Deposit date: | 2003-09-12 | Release date: | 2004-09-28 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1 J.Mol.Biol., 342, 2004
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6M3X
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![BU of 6m3x by Molmil](/molmil-images/mine/6m3x) | Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii | Descriptor: | FE (III) ION, Sulfur oxygenase/reductase | Authors: | Sato, Y, Adachi, N, Moriya, T, Arakawa, T, Kawasaki, M, Yamada, C, Senda, T, Fushinobu, S. | Deposit date: | 2020-03-04 | Release date: | 2020-07-15 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (2.24 Å) | Cite: | Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase fromSulfurisphaera tokodaii. J Struct Biol X, 4, 2020
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8JW3
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![BU of 8jw3 by Molmil](/molmil-images/mine/8jw3) | The crystal structure of the viral terpene synthase from Orpheovirus IHUMI-LCC2 | Descriptor: | SULFATE ION, Terpenoid synthase | Authors: | Jung, Y, Mitsuhashi, T, Senda, M, Sato, S, Senda, T, Fujita, M. | Deposit date: | 2023-06-28 | Release date: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome. J.Am.Chem.Soc., 145, 2023
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7WAD
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![BU of 7wad by Molmil](/molmil-images/mine/7wad) | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS | Descriptor: | Cyanophycin synthase, MAGNESIUM ION, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER | Authors: | Kawasaki, M, Miyakawa, T, Yang, J, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | Deposit date: | 2021-12-14 | Release date: | 2022-09-07 | Last modified: | 2022-09-14 | Method: | ELECTRON MICROSCOPY (2.96 Å) | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Nat Commun, 13, 2022
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7WAE
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![BU of 7wae by Molmil](/molmil-images/mine/7wae) | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS, 4x(beta-Asp-Arg), and aspartate | Descriptor: | 4x(beta-Asp-Arg), ARGININE, ASPARTIC ACID, ... | Authors: | Miyakawa, T, Yang, J, Kawasaki, M, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | Deposit date: | 2021-12-14 | Release date: | 2022-09-07 | Last modified: | 2022-09-14 | Method: | ELECTRON MICROSCOPY (2.64 Å) | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Nat Commun, 13, 2022
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7WAC
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![BU of 7wac by Molmil](/molmil-images/mine/7wac) | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) | Descriptor: | Cyanophycin synthase | Authors: | Kawasaki, M, Miyakawa, T, Yang, J, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | Deposit date: | 2021-12-14 | Release date: | 2022-09-07 | Last modified: | 2022-09-14 | Method: | ELECTRON MICROSCOPY (2.91 Å) | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Nat Commun, 13, 2022
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7WAF
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![BU of 7waf by Molmil](/molmil-images/mine/7waf) | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS and 4x(beta-Asp-Arg) | Descriptor: | 4x(beta-Asp-Arg), ARGININE, Cyanophycin synthase, ... | Authors: | Miyakawa, T, Yang, J, Kawasaki, M, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | Deposit date: | 2021-12-14 | Release date: | 2022-09-07 | Last modified: | 2022-09-14 | Method: | ELECTRON MICROSCOPY (2.52 Å) | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Nat Commun, 13, 2022
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