8YE0
 
 | | Crystal structure of KgpF prenyltransferase | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, LynF/TruF/PatF family peptide O-prenyltransferase, MAGNESIUM ION, ... | | Authors: | Hamada, K, Inoue, S, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2024-02-21 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | De Novo Discovery of Pseudo-Natural Prenylated Macrocyclic Peptide Ligands.
Angew.Chem.Int.Ed.Engl., 2024
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5XFE
 | | Luciferin-regenerating enzyme solved by SAD using XFEL (refined against 11,000 patterns) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2017-04-10 | | Release date: | 2017-08-30 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
IUCrJ, 4, 2017
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8WM0
 | | Crystal structure of TNIK-thiopeptide wTP3 complex | | Descriptor: | ADENOSINE, THIOPEPTIDE wTP3, TRAF2 and NCK-interacting protein kinase | | Authors: | Hamada, K, Kobayashi, S, Vinogradov, A.A, Zhang, Y, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2023-10-01 | | Release date: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides.
J.Am.Chem.Soc., 2024
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1UCQ
 | | Crystal structure of the L intermediate of bacteriorhodopsin | | Descriptor: | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, RETINAL, ... | | Authors: | Kouyama, T, Nishikawa, T, Tokuhisa, T, Okumura, H. | | Deposit date: | 2003-04-17 | | Release date: | 2003-12-30 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle.
J.Mol.Biol., 335, 2004
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8SKM
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1K5C
 | | Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ENDOPOLYGALACTURONASE, ... | | Authors: | Shimizu, T, Nakatsu, T, Miyairi, K, Okuno, T, Kato, H. | | Deposit date: | 2001-10-10 | | Release date: | 2002-06-05 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (0.96 Å) | | Cite: | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Biochemistry, 41, 2002
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5D9B
 | | Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
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5D9D
 | | Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
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5D9C
 | | Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | | Deposit date: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
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1KCD
 | | Endopolygalacturonase I from Stereum purpureum complexed with two galacturonate at 1.15 A resolution. | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ENDOPOLYGALACTURONASE, ... | | Authors: | Shimizu, T, Nakatsu, T, Miyairi, K, Okuno, T, Kato, H. | | Deposit date: | 2001-11-08 | | Release date: | 2002-06-05 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.15 Å) | | Cite: | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Biochemistry, 41, 2002
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1KCC
 | | Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution. | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ENDOPOLYGALACTURONASE, ... | | Authors: | Shimizu, T, Nakatsu, T, Miyairi, K, Okuno, T, Kato, H. | | Deposit date: | 2001-11-08 | | Release date: | 2002-06-05 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Biochemistry, 41, 2002
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8GUJ
 | | Bre1-nucleosome complex (Model II) | | Descriptor: | DNA (147-mer), E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B, ... | | Authors: | Onishi, S, Sato, K, Hamada, K, Nishizawa, T, Nureki, O, Ogata, K, Sengoku, T. | | Deposit date: | 2022-09-12 | | Release date: | 2023-09-20 | | Last modified: | 2024-04-03 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Structure of the human Bre1 complex bound to the nucleosome.
Nat Commun, 15, 2024
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8GUI
 | | Bre1-nucleosome complex (Model I) | | Descriptor: | DNA (147-mer), E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B, ... | | Authors: | Onishi, S, Hamada, K, Sato, K, Nishizawa, T, Nureki, O, Ogata, K, Sengoku, T. | | Deposit date: | 2022-09-12 | | Release date: | 2023-09-20 | | Last modified: | 2024-04-03 | | Method: | ELECTRON MICROSCOPY (2.81 Å) | | Cite: | Structure of the human Bre1 complex bound to the nucleosome.
Nat Commun, 15, 2024
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8GUK
 | | Human nucleosome core particle (free form) | | Descriptor: | DNA (147-mer), Histone H2A type 1, Histone H2B type 1-J, ... | | Authors: | Onishi, S, Sato, K, Nishizawa, T, Nureki, O, Ogata, K, Sengoku, T. | | Deposit date: | 2022-09-12 | | Release date: | 2023-09-20 | | Last modified: | 2024-04-03 | | Method: | ELECTRON MICROSCOPY (2.51 Å) | | Cite: | Structure of the human Bre1 complex bound to the nucleosome.
Nat Commun, 15, 2024
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6LKD
 | | in meso full-length rat KMO in complex with a pyrazoyl benzoic acid inhibitor | | Descriptor: | 5-[5-(4-chloranyl-3-fluoranyl-phenyl)-4-methyl-pyrazol-1-yl]-2-phenylmethoxy-benzoic acid, CHLORIDE ION, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Mimasu, S, Yamagishi, H, Kiyohara, M, Kakefuda, K, Okuda, T. | | Deposit date: | 2019-12-19 | | Release date: | 2020-12-23 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Full-length in meso structure and mechanism of rat kynurenine 3-monooxygenase inhibition.
Commun Biol, 4, 2021
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6LKE
 | | in meso full-length rat KMO in complex with an inhibitor identified via DNA-encoded chemical library screening | | Descriptor: | 4-chloranyl-2-[[5-chloranyl-2-(5-methoxy-1,3-dihydroisoindol-2-yl)-1,3-thiazol-4-yl]carbonyl-methyl-amino]-5-fluoranyl-benzoic acid, CHLORIDE ION, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Mimasu, S, Yamagishi, H, Kiyohara, M, Hupp, D.C, Liu, J, Kakefuda, K, Okuda, T. | | Deposit date: | 2019-12-19 | | Release date: | 2020-12-23 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Full-length in meso structure and mechanism of rat kynurenine 3-monooxygenase inhibition.
Commun Biol, 4, 2021
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7VMY
 | | Crystal structure of LimF prenyltransferase bound with GSPP | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GERANYL S-THIOLODIPHOSPHATE, LynF/TruF/PatF family peptide O-prenyltransferase, ... | | Authors: | Hamada, K, Kobayashi, S, Okada, C, Zhang, Y, Inoue, S, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates
Nat Catal, 2022
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7VMW
 | | Crystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP | | Descriptor: | GERANYL S-THIOLODIPHOSPHATE, LynF/TruF/PatF family peptide O-prenyltransferase, MAGNESIUM ION, ... | | Authors: | Hamada, K, Kobayashi, S, Okada, C, Zhang, Y, Inoue, S, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates
Nat Catal, 2022
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7XZR
 | | Crystal structure of TNIK-AMPPNP-thiopeptide TP15 complex | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, SULFATE ION, ... | | Authors: | Hamada, K, Vinogradov, A.A, Zhang, Y, Chang, J.S, Nishimura, H, Goto, Y, Onaka, H, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-26 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144, 2022
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7XZQ
 | | Crystal structure of TNIK-thiopeptide TP1 complex | | Descriptor: | 1,4-BUTANEDIOL, TRAF2 and NCK-interacting protein kinase, thiopeptide TP1 | | Authors: | Hamada, K, Vinogradov, A.A, Zhang, Y, Chang, J.S, Nishimura, H, Goto, Y, Onaka, H, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144, 2022
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3X05
 | | Crystal structure of PIP4KIIBETA T201M complex with AMP | | Descriptor: | ADENOSINE MONOPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Lo, Y.H, Sumita, K, Senda, M, Terakawa, J, Dimitoris, A, Locasale, J.W, Sasaki, M, Yoshino, H, Zhang, Y, Kahoud, E.R, Takano, T, Yokota, T, Emerling, B, Asara, J.A, Ishida, T, Shimada, I, Daikoku, T, Cantley, L.C, Senda, T, Sasaki, A.T. | | Deposit date: | 2014-10-09 | | Release date: | 2015-10-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Mol.Cell, 61, 2016
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3X06
 | | Crystal structure of PIP4KIIBETA T201M complex with GMP | | Descriptor: | GUANOSINE-5'-MONOPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Lo, Y.H, Sumita, K, Senda, M, Terakawa, J, Dimitoris, A, Locasale, J.W, Sasaki, M, Yoshino, H, Zhang, Y, Kahoud, E.R, Takano, T, Yokota, T, Emerling, B, Asara, J.A, Ishida, T, Shimada, I, Daikoku, T, Cantley, L.C, Senda, T, Sasaki, A.T. | | Deposit date: | 2014-10-09 | | Release date: | 2015-10-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Mol.Cell, 61, 2016
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3X03
 | | Crystal structure of PIP4KIIBETA complex with AMPPNP | | Descriptor: | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Lo, Y.H, Sumita, K, Senda, M, Terakawa, J, Dimitoris, A, Locasale, J.W, Sasaki, M, Yoshino, H, Zhang, Y, Kahoud, E.R, Takano, T, Yokota, T, Emerling, B, Asara, J.A, Ishida, T, Shimada, I, Daikoku, T, Cantley, L.C, Senda, T, Sasaki, A.T. | | Deposit date: | 2014-10-09 | | Release date: | 2015-10-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Mol.Cell, 61, 2016
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3X01
 | | Crystal structure of PIP4KIIBETA complex with AMP | | Descriptor: | ADENOSINE MONOPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Lo, Y.H, Sumita, K, Senda, M, Terakawa, J, Dimitoris, A, Locasale, J.W, Sasaki, M, Yoshino, H, Zhang, Y, Kahoud, E.R, Takano, T, Yokota, T, Emerling, B, Asara, J.A, Ishida, T, Shimada, I, Daikoku, T, Cantley, L.C, Senda, T, Sasaki, A.T. | | Deposit date: | 2014-10-09 | | Release date: | 2015-10-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Mol.Cell, 61, 2016
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3X09
 | | Crystal structure of PIP4KIIBETA F205L complex with AMP | | Descriptor: | ADENOSINE MONOPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | | Authors: | Takeuchi, K, Lo, Y.H, Sumita, K, Senda, M, Terakawa, J, Dimitoris, A, Locasale, J.W, Sasaki, M, Yoshino, H, Zhang, Y, Kahoud, E.R, Takano, T, Yokota, T, Emerling, B, Asara, J.A, Ishida, T, Shimada, I, Daikoku, T, Cantley, L.C, Senda, T, Sasaki, A.T. | | Deposit date: | 2014-10-09 | | Release date: | 2015-10-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Mol.Cell, 61, 2016
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