8YE0
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![BU of 8ye0 by Molmil](/molmil-images/mine/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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5GUG
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![BU of 5gug by Molmil](/molmil-images/mine/5gug) | Crystal structure of inositol 1,4,5-trisphosphate receptor large cytosolic domain with inositol 1,4,5-trisphosphate | Descriptor: | D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, Inositol 1,4,5-trisphosphate receptor type 1 | Authors: | Hamada, K, Miyatake, H, Terauchi, A, Mikoshiba, K. | Deposit date: | 2016-08-29 | Release date: | 2017-04-26 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (7.399 Å) | Cite: | IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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8WM0
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![BU of 8wm0 by Molmil](/molmil-images/mine/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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1GC7
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![BU of 1gc7 by Molmil](/molmil-images/mine/1gc7) | CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN | Descriptor: | RADIXIN | Authors: | Hamada, K, Shimizu, T, Matsui, T, Tsukita, S, Tsukita, S, Hakoshima, T. | Deposit date: | 2000-07-21 | Release date: | 2000-09-20 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain. EMBO J., 19, 2000
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1GC6
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![BU of 1gc6 by Molmil](/molmil-images/mine/1gc6) | CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN COMPLEXED WITH INOSITOL-(1,4,5)-TRIPHOSPHATE | Descriptor: | D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, RADIXIN | Authors: | Hamada, K, Shimizu, T, Matsui, T, Tsukita, S, Tsukita, S, Hakoshima, T. | Deposit date: | 2000-07-21 | Release date: | 2000-09-20 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain. EMBO J., 19, 2000
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5XA0
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![BU of 5xa0 by Molmil](/molmil-images/mine/5xa0) | Crystal structure of inositol 1,4,5-trisphosphate receptor cytosolic domain | Descriptor: | Inositol 1,4,5-trisphosphate receptor type 1 | Authors: | Hamada, K, Miyatake, H, Terauchi, A, Mikoshiba, K. | Deposit date: | 2017-03-10 | Release date: | 2017-04-19 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (5.812 Å) | Cite: | IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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5XA1
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![BU of 5xa1 by Molmil](/molmil-images/mine/5xa1) | Crystal structure of inositol 1,4,5-trisphosphate receptor cytosolic domain with inositol 1,4,5-trisphosphate | Descriptor: | D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, Inositol 1,4,5-trisphosphate receptor type 1 | Authors: | Hamada, K, Miyatake, H, Terauchi, A, Mikoshiba, K. | Deposit date: | 2017-03-10 | Release date: | 2017-04-19 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (6.204 Å) | Cite: | IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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5X9Z
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![BU of 5x9z by Molmil](/molmil-images/mine/5x9z) | Crystal structure of inositol 1,4,5-trisphosphate receptor large cytosolic domain | Descriptor: | Inositol 1,4,5-trisphosphate receptor type 1 | Authors: | Hamada, K, Miyatake, H, Terauchi, A, Mikoshiba, K. | Deposit date: | 2017-03-10 | Release date: | 2017-04-19 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (7.311 Å) | Cite: | IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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1J19
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![BU of 1j19 by Molmil](/molmil-images/mine/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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1SRP
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![BU of 1srp by Molmil](/molmil-images/mine/1srp) | STRUCTURAL ANALYSIS OF SERRATIA PROTEASE | Descriptor: | CALCIUM ION, SERRALYSIN, ZINC ION | Authors: | Hamada, K, Hiramatsu, H, Katsuya, Y, Hata, Y, Katsube, Y. | Deposit date: | 1994-11-02 | Release date: | 1995-02-14 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a beta-sheet coil motif at 2.0 A resolution. J.Biochem.(Tokyo), 119, 1996
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7VMY
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![BU of 7vmy by Molmil](/molmil-images/mine/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
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![BU of 7vmw by Molmil](/molmil-images/mine/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
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![BU of 7xzr by Molmil](/molmil-images/mine/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
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![BU of 7xzq by Molmil](/molmil-images/mine/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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8JE4
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![BU of 8je4 by Molmil](/molmil-images/mine/8je4) | Crystal structure of LimF prenyltransferase (H239G/W273T mutant) bound with the thiodiphosphate moiety of farnesyl S-thiolodiphosphate (FSPP) | Descriptor: | MAGNESIUM ION, TRIHYDROGEN THIODIPHOSPHATE, prenyltransferase, ... | Authors: | Hamada, K, Oguni, A, Zhang, Y, Satake, M, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | Deposit date: | 2023-05-15 | Release date: | 2023-11-08 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.19 Å) | Cite: | Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases. J.Am.Chem.Soc., 145, 2023
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1UJB
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![BU of 1ujb by Molmil](/molmil-images/mine/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
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![BU of 1ujc by Molmil](/molmil-images/mine/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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1UJ4
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![BU of 1uj4 by Molmil](/molmil-images/mine/1uj4) | Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase | Descriptor: | CHLORIDE ION, ribose 5-phosphate isomerase | Authors: | Hamada, K, Ago, H, Sugahara, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-26 | Release date: | 2004-07-13 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi) J.Biol.Chem., 278, 2003
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1UJ6
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![BU of 1uj6 by Molmil](/molmil-images/mine/1uj6) | Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with arabinose-5-phosphate | Descriptor: | ARABINOSE-5-PHOSPHATE, CHLORIDE ION, ribose 5-phosphate isomerase | Authors: | Hamada, K, Ago, H, Sugahara, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-26 | Release date: | 2004-07-13 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.74 Å) | Cite: | Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi) J.Biol.Chem., 278, 2003
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1UJ5
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![BU of 1uj5 by Molmil](/molmil-images/mine/1uj5) | Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with ribose-5-phosphate | Descriptor: | CHLORIDE ION, RIBULOSE-5-PHOSPHATE, ribose 5-phosphate isomerase | Authors: | Hamada, K, Ago, H, Sugahara, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-26 | Release date: | 2004-07-13 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi) J.Biol.Chem., 278, 2003
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1UKW
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![BU of 1ukw by Molmil](/molmil-images/mine/1ukw) | Crystal structure of medium-chain acyl-CoA dehydrogenase from Thermus thermophilus HB8 | Descriptor: | COBALT (II) ION, FLAVIN-ADENINE DINUCLEOTIDE, acyl-CoA dehydrogenase | Authors: | Hamada, K, Ago, H, Kuramitsu, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-09-02 | Release date: | 2004-11-09 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of Thermus thermophilus medium-chain acyl-CoA dehydrogenase To be published
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256B
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![BU of 256b by Molmil](/molmil-images/mine/256b) | |
8GUJ
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![BU of 8guj by Molmil](/molmil-images/mine/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
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![BU of 8gui by Molmil](/molmil-images/mine/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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1WMW
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![BU of 1wmw by Molmil](/molmil-images/mine/1wmw) | Crystal structure of geranulgeranyl diphosphate synthase from Thermus thermophilus | Descriptor: | geranylgeranyl diphosphate synthetase | Authors: | Suto, K, Nishio, K, Nodake, Y, Hamada, K, Kawamoto, M, Nakagawa, N, Kuramitu, S, Miura, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2004-07-21 | Release date: | 2005-07-21 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Crystal structure of geranulgeranyl diphosphate synthase from Thermus thermophilus To be Published
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