8J2Q
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7WYR
| Crystal structure of Cypovirus Polyhedra mutant fused with CLN025 | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Polyhedrin fused with CLN025 | Authors: | Kojima, M, Abe, S, Hirata, K, Yamashita, K, Ueno, T. | Deposit date: | 2022-02-16 | Release date: | 2023-02-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein. Biomater Sci, 11, 2023
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8W7N
| Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis | Descriptor: | Pesticidal crystal protein Cry1Aa, UNKNOWN ATOM OR ION | Authors: | Tanaka, J, Abe, S, Hayakawa, T, Kojima, M, Yamashita, K, Hirata, K, Ueno, T. | Deposit date: | 2023-08-31 | Release date: | 2024-03-06 | Method: | X-RAY DIFFRACTION (3.6 Å) | Cite: | Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis. Biochem.Biophys.Res.Commun., 685, 2023
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8IJU
| ATP-dependent RNA helicase DDX39A (URH49delta41) | Descriptor: | 1,2-ETHANEDIOL, ATP-dependent RNA helicase DDX39A, PHOSPHATE ION, ... | Authors: | Mikami, B, Fujita, K, Masuda, S, Kojima, M. | Deposit date: | 2023-02-28 | Release date: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.82 Å) | Cite: | Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes. Nat Commun, 15, 2024
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1IYY
| NMR STRUCTURE OF Gln25-RIBONUCLEASE T1, 24 STRUCTURES | Descriptor: | RIBONUCLEASE T1 | Authors: | Hatano, K, Kojima, M, Suzuki, E, Tanokura, M, Takahashi, K. | Deposit date: | 2002-09-12 | Release date: | 2003-10-07 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Determination of the NMR structure of Gln25-ribonuclease T1. Biol. Chem., 384, 2003
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1Y43
| crystal structure of aspergilloglutamic peptidase from Aspergillus niger | Descriptor: | Aspergillopepsin II heavy chain, Aspergillopepsin II light chain, SULFATE ION | Authors: | Sasaki, H, Nakagawa, A, Iwata, S, Muramatsu, T, Suganuma, M, Sawano, Y, Kojima, M, Kubota, K, Takahashi, K. | Deposit date: | 2004-11-30 | Release date: | 2005-12-13 | Last modified: | 2013-02-27 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger Proc.Jpn.Acad.,Ser.B, 80, 2004
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2CII
| The crystal structure of H-2Db complexed with a partial peptide epitope suggests an MHC Class I assembly-intermediate | Descriptor: | BETA-2-MICROGLOBULIN, GLYCEROL, H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN D-B ALPHA CHAIN, ... | Authors: | Glithero, A, Tormo, J, Doering, K, Kojima, M, Jones, E.Y, Elliott, T. | Deposit date: | 2006-03-21 | Release date: | 2006-03-29 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | The crystal structure of H-2D(b) complexed with a partial peptide epitope suggests a major histocompatibility complex class I assembly intermediate. J. Biol. Chem., 281, 2006
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6KS2
| Structure of anti-Ghrelin receptor antibody | Descriptor: | Fab7881 Heavy Chain (FabH), Fab7881 Light Chain (FabL) | Authors: | Shiimura, Y, Horita, S, Asada, H, Hirata, K, Iwata, S, Kojima, M. | Deposit date: | 2019-08-23 | Release date: | 2020-08-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.753 Å) | Cite: | Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode. Nat Commun, 11, 2020
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6KO5
| Complex structure of Ghrelin receptor with Fab | Descriptor: | 6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one, Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1, Fab7881 Heavy Chain, ... | Authors: | Shiimura, Y, Horita, S, Asada, H, Hirata, K, Iwata, S, Kojima, M. | Deposit date: | 2019-08-08 | Release date: | 2020-08-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode. Nat Commun, 11, 2020
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7XHS
| Crystal structure of CipA crystal produced by cell-free protein synthesis | Descriptor: | Cro/Cl family transcriptional regulator | Authors: | Abe, S, Tanaka, J, Kojima, M, Kanamaru, S, Yamashita, K, Hirata, K, Ueno, T. | Deposit date: | 2022-04-10 | Release date: | 2023-02-01 | Method: | X-RAY DIFFRACTION (2.11 Å) | Cite: | Cell-free protein crystallization for nanocrystal structure determination. Sci Rep, 12, 2022
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7XWS
| Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis with small volume | Descriptor: | ACETYL GROUP, CHLORIDE ION, Polyhedrin | Authors: | Abe, S, Tanaka, J, Kojima, M, Hirata, K, Yamashita, K, Ueno, T. | Deposit date: | 2022-05-27 | Release date: | 2023-02-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Cell-free protein crystallization for nanocrystal structure determination. Sci Rep, 12, 2022
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7XHR
| Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis | Descriptor: | ACETYL GROUP, CHLORIDE ION, Polyhedrin | Authors: | Abe, S, Tanaka, J, Kojima, M, Hirata, K, Yamashita, K, Ueno, T. | Deposit date: | 2022-04-10 | Release date: | 2023-02-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.801 Å) | Cite: | Cell-free protein crystallization for nanocrystal structure determination. Sci Rep, 12, 2022
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3TRS
| The crystal structure of aspergilloglutamic peptidase from Aspergillus niger | Descriptor: | Aspergillopepsin-2 heavy chain, Aspergillopepsin-2 light chain, DIMETHYL SULFOXIDE | Authors: | Sasaki, H, Kubota, K, Lee, W.C, Ohtsuka, J, Kojima, M, Takahashi, K, Tanokura, M. | Deposit date: | 2011-09-10 | Release date: | 2012-08-22 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis. J.Biochem., 152, 2012
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1BI6
| NMR STRUCTURE OF BROMELAIN INHIBITOR VI FROM PINEAPPLE STEM | Descriptor: | BROMELAIN INHIBITOR VI | Authors: | Hatano, K.-I. | Deposit date: | 1995-12-07 | Release date: | 1996-04-03 | Last modified: | 2017-11-29 | Method: | SOLUTION NMR | Cite: | Solution structure of bromelain inhibitor IV from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean. Biochemistry, 35, 1996
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7YV1
| Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Isoform 2B of GTPase KRas, KA30L Fab H-chain, ... | Authors: | Irie, M, Fukami, T.A, Matsuo, A, Saka, K, Nishimura, M, Saito, H, Torizawa, T, Tanada, M, Ohta, A. | Deposit date: | 2022-08-18 | Release date: | 2023-07-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.454 Å) | Cite: | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. J.Am.Chem.Soc., 145, 2023
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2BI6
| NMR STUDY OF BROMELAIN INHIBITOR VI FROM PINEAPPLE STEM | Descriptor: | BROMELAIN INHIBITOR VI | Authors: | Hatano, K.-I. | Deposit date: | 1995-12-07 | Release date: | 1996-04-03 | Last modified: | 2017-11-29 | Method: | SOLUTION NMR | Cite: | Solution structure of bromelain inhibitor IV from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean. Biochemistry, 35, 1996
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7YUZ
| Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784 | Descriptor: | AP8784, GUANOSINE-5'-DIPHOSPHATE, IODIDE ION, ... | Authors: | Irie, M, Fukami, T.A, Tanada, M, Ohta, A, Torizawa, T. | Deposit date: | 2022-08-18 | Release date: | 2023-07-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.878 Å) | Cite: | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. J.Am.Chem.Soc., 145, 2023
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3IWR
| Crystal structure of class I chitinase from Oryza sativa L. japonica | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Chitinase | Authors: | Kezuka, Y, Watanabe, T, Nonaka, T. | Deposit date: | 2009-09-03 | Release date: | 2010-04-21 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.57 Å) | Cite: | Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Proteins, 78, 2010
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5X9A
| Crystal structure of calaxin with calcium | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, Calaxin | Authors: | Shojima, T, Hou, F, Takahashi, Y, Okai, M, Mizuno, K, Inaba, K, Miyakawa, T, Tanokura, M. | Deposit date: | 2017-03-06 | Release date: | 2018-03-14 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition Sci Rep, 8, 2018
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5YPX
| Crystal structure of calaxin with magnesium | Descriptor: | Calaxin, MAGNESIUM ION | Authors: | Shojima, T, Hou, F, Takahashi, Y, Okai, M, Mizuno, K, Inaba, K, Miyakawa, T, Tanokura, M. | Deposit date: | 2017-11-04 | Release date: | 2018-03-14 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.64 Å) | Cite: | Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition Sci Rep, 8, 2018
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6C80
| Crystal structure of a flax cytokinin oxidase | Descriptor: | 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, AMMONIUM ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Wan, L, Williams, S, Kobe, B. | Deposit date: | 2018-01-23 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Structural and functional insights into the modulation of the activity of a flax cytokinin oxidase by flax rust effector AvrL567-A. Mol. Plant Pathol., 20, 2019
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7EKD
| Crystal structure of gibberellin 3-oxidase 2 (GA3ox2) in rice | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-OXOGLUTARIC ACID, Gibberellin 3-beta-dioxygenase 2, ... | Authors: | Takehara, S, Kawai, K, Mikami, B, Ueguchi-Tanaka, M. | Deposit date: | 2021-04-05 | Release date: | 2022-02-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.899 Å) | Cite: | Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza. Commun Biol, 5, 2022
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7E18
| Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53 | Descriptor: | 1,2-ETHANEDIOL, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1ab | Authors: | Senda, M, Konno, S, Hayashi, Y, Senda, T. | Deposit date: | 2021-02-01 | Release date: | 2021-06-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents. J.Med.Chem., 65, 2022
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7E19
| Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5 | Descriptor: | (phenylmethyl) N-[(2S)-1-[[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate, 3C-like proteinase | Authors: | Senda, M, Konno, S, Hayashi, Y, Senda, T. | Deposit date: | 2021-02-01 | Release date: | 2021-06-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents. J.Med.Chem., 65, 2022
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2DKV
| Crystal structure of class I chitinase from Oryza sativa L. japonica | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, chitinase | Authors: | Kezuka, Y, Nishizawa, Y, Watanabe, T, Nonaka, T. | Deposit date: | 2006-04-14 | Release date: | 2007-05-01 | Last modified: | 2020-01-01 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Proteins, 78, 2010
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