4YSU
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![BU of 4ysu by Molmil](/molmil-images/mine/4ysu) | Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 25.0 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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4YSA
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![BU of 4ysa by Molmil](/molmil-images/mine/4ysa) | Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans | Descriptor: | COPPER (II) ION, Nitrite reductase, SODIUM 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: | 2016-02-24 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.43 Å) | Cite: | Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography J.Biochem., 159, 2016
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4YSO
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![BU of 4yso by Molmil](/molmil-images/mine/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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3X2S
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![BU of 3x2s by Molmil](/molmil-images/mine/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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4YSR
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![BU of 4ysr by Molmil](/molmil-images/mine/4ysr) | Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.6 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 (1.34 Å) | Cite: | Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography J.Biochem., 159, 2016
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1WTJ
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![BU of 1wtj by Molmil](/molmil-images/mine/1wtj) | Crystal Structure of delta1-piperideine-2-carboxylate reductase from Pseudomonas syringae pvar.tomato | Descriptor: | ureidoglycolate dehydrogenase | Authors: | Goto, M, Muramatsu, H, Mihara, H, Kurihara, T, Esaki, N, Omi, R, Miyahara, I, Hirotsu, K. | Deposit date: | 2004-11-24 | Release date: | 2005-10-04 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.55 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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4Z34
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![BU of 4z34 by Molmil](/molmil-images/mine/4z34) | Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307 | Descriptor: | (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate, Lysophosphatidic acid receptor 1, Soluble cytochrome b562, ... | Authors: | Chrencik, J.E, Roth, C.B, Terakado, M, Kurata, H, Omi, R, Kihara, Y, Warshaviak, D, Nakade, S, Asmar-Rovira, G, Mileni, M, Mizuno, H, Griffith, M.T, Rodgers, C, Han, G.W, Velasquez, J, Chun, J, Stevens, R.C, Hanson, M.A, GPCR Network (GPCR) | Deposit date: | 2015-03-30 | Release date: | 2015-06-03 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1. Cell, 161, 2015
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1WMJ
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![BU of 1wmj by Molmil](/molmil-images/mine/1wmj) | |
5Y5F
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![BU of 5y5f by Molmil](/molmil-images/mine/5y5f) | Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | Authors: | Tosha, T, Nomura, T, Nishida, T, Ueno, G, Murakami, H, Yamashita, K, Hirata, K, Yamamoto, M, Ago, H, Sugimoto, H, Shiro, Y, Kubo, M. | Deposit date: | 2017-08-09 | Release date: | 2017-12-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate. Nat Commun, 8, 2017
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1DRN
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![BU of 1drn by Molmil](/molmil-images/mine/1drn) | NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC) | Descriptor: | DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3'), DNA/RNA (5'-D(*GP*GP*AP*GP*A)-R(P*UP*GP*AP*C)-3') | Authors: | Nishizaki, T, Iwai, S, Ohkubo, T, Kojima, C, Nakamura, H, Kyogoku, Y, Ohtsuka, E. | Deposit date: | 1995-11-15 | Release date: | 1996-04-03 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). Biochemistry, 35, 1996
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5Y5G
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![BU of 5y5g by Molmil](/molmil-images/mine/5y5g) | Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | Authors: | Tosha, T, Nomura, T, Nishida, T, Ueno, G, Murakami, H, Yamashita, K, Hirata, K, Yamamoto, M, Ago, H, Sugimoto, H, Shiro, Y, Kubo, M. | Deposit date: | 2017-08-09 | Release date: | 2017-12-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate. Nat Commun, 8, 2017
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1DHH
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![BU of 1dhh by Molmil](/molmil-images/mine/1dhh) | NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC) | Descriptor: | DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3'), DNA/RNA (5'-D(*GP*G)-R(P*AP*GP*AP*U)-D(P*GP*AP*C)-3') | Authors: | Nishizaki, T, Iwai, S, Ohkubo, T, Kojima, C, Nakamura, H, Kyogoku, Y, Ohtsuka, E. | Deposit date: | 1995-10-18 | Release date: | 1996-04-03 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). Biochemistry, 35, 1996
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5B1Y
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![BU of 5b1y by Molmil](/molmil-images/mine/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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7W7C
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![BU of 7w7c by Molmil](/molmil-images/mine/7w7c) | Heme exporter in the unliganded form | Descriptor: | Putative ABC transport system integral membrane protein, Putative ABC transport system, ATP-binding protein, ... | Authors: | Rahman, M.M, Hisano, T, Nakamura, H, Tosha, T, Shirouzu, M, Shiro, Y. | Deposit date: | 2021-12-04 | Release date: | 2022-06-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria. Proc.Natl.Acad.Sci.USA, 119, 2022
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1Y56
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![BU of 1y56 by Molmil](/molmil-images/mine/1y56) | Crystal structure of L-proline dehydrogenase from P.horikoshii | Descriptor: | 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | Authors: | Tsuge, H, Kawakami, R, Sakuraba, H, Ago, H, Miyano, M, Aki, K, Katunuma, N, Ohshima, T. | Deposit date: | 2004-12-02 | Release date: | 2005-07-26 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.86 Å) | Cite: | Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii J.Biol.Chem., 280, 2005
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1GZA
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![BU of 1gza by Molmil](/molmil-images/mine/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: | 2020-07-29 | 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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1QM8
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![BU of 1qm8 by Molmil](/molmil-images/mine/1qm8) | Structure of Bacteriorhodopsin at 100 K | Descriptor: | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL, ... | Authors: | Takeda, K, Matsui, Y, Sato, H, Hino, T, Kanamori, E, Okumura, H, Yamane, T, Kamiya, N, Kouyama, T. | Deposit date: | 1999-09-22 | Release date: | 2000-08-16 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies. J.Mol.Biol., 283, 1998
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1HSR
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![BU of 1hsr by Molmil](/molmil-images/mine/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: | 2020-07-29 | 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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1WSF
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![BU of 1wsf by Molmil](/molmil-images/mine/1wsf) | Co-crystal structure of E.coli RNase HI active site mutant (D134A*) with Mn2+ | Descriptor: | MANGANESE (II) ION, Ribonuclease HI | Authors: | Tsunaka, Y, Takano, K, Matsumura, H, Yamagata, Y, Kanaya, S. | Deposit date: | 2004-11-05 | Release date: | 2005-02-08 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Identification of Single Mn(2+) Binding Sites Required for Activation of the Mutant Proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray Crystallography J.Mol.Biol., 345, 2005
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1WDD
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![BU of 1wdd by Molmil](/molmil-images/mine/1wdd) | Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | Authors: | Mizohata, E, Matsumura, H, Ueno, T, Ishida, H, Inoue, T, Makino, A, Mae, T, Kai, Y. | Deposit date: | 2004-05-13 | Release date: | 2004-11-13 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.35 Å) | Cite: | Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate J.Mol.Biol., 422, 2012
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1WTG
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![BU of 1wtg by Molmil](/molmil-images/mine/1wtg) | Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-biphenylalanine-Gln-p-aminobenzamidine | Descriptor: | 2-(3-BIPHENYL-4-YL-2-ETHANESULFONYLAMINO-PROPIONYLAMINO)-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIMIDOYL-BENZYLAMIDE), CALCIUM ION, Coagulation factor VII, ... | Authors: | Kadono, S, Sakamoto, S, Kikuchi, Y, Oh-Eda, M, Yabuta, N, Kitazawa, K, Yoshihashi, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Kodama, M, Haramura, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T. | Deposit date: | 2004-11-23 | Release date: | 2005-11-23 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Novel interactions of large P3 moiety and small P4 moiety in the binding of the peptide mimetic factor VIIa inhibitor Biochem.Biophys.Res.Commun., 326, 2005
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1WN7
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![BU of 1wn7 by Molmil](/molmil-images/mine/1wn7) | Crystal structure of archaeal family B DNA polymerase mutant | Descriptor: | Family B DNA Polymerase, GLYCEROL, NICKEL (II) ION | Authors: | Kuroita, T, Matsumura, H, Yokota, N, Hashimoto, H, Imanaka, T, Inoue, T, Kai, Y. | Deposit date: | 2004-07-28 | Release date: | 2005-08-02 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Structural Mechanism for Coordination of Proofreading and Polymerase Activities in Archaeal DNA Polymerases J.Mol.Biol., 351, 2005
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1WSG
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![BU of 1wsg by Molmil](/molmil-images/mine/1wsg) | Co-crystal structure of E.coli RNase HI active site mutant (E48A/D134N*) with Mn2+ | Descriptor: | MANGANESE (II) ION, Ribonuclease HI | Authors: | Tsunaka, Y, Takano, K, Matsumura, H, Yamagata, Y, Kanaya, S. | Deposit date: | 2004-11-05 | Release date: | 2005-02-08 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Identification of Single Mn(2+) Binding Sites Required for Activation of the Mutant Proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray Crystallography J.Mol.Biol., 345, 2005
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5XVD
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![BU of 5xvd by Molmil](/molmil-images/mine/5xvd) | [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an air-oxidized condition | Descriptor: | FE3-S4 CLUSTER, FE4-S4-O CLUSTER, GLYCEROL, ... | Authors: | Nishikawa, K, Matsuura, H, Muhd Noor, N.D, Tai, H, Hirota, S, Kim, J, Kang, J, Tateno, M, Yoon, K.S, Ogo, S, Shomura, Y, Higuchi, Y. | Deposit date: | 2017-06-27 | Release date: | 2018-06-27 | Last modified: | 2019-07-10 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2. Chem.Commun.(Camb.), 54, 2018
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5XVB
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![BU of 5xvb by Molmil](/molmil-images/mine/5xvb) | [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition | Descriptor: | FE3-S4 CLUSTER, GLYCEROL, IRON/SULFUR CLUSTER, ... | Authors: | Nishikawa, K, Matsuura, H, Muhd Noor, N.D, Tai, H, Hirota, S, Kim, J, Kang, J, Tateno, M, Yoon, K.S, Ogo, S, Shomura, Y, Higuchi, Y. | Deposit date: | 2017-06-27 | Release date: | 2018-06-27 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2. Chem.Commun.(Camb.), 54, 2018
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