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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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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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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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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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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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
 | | 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
 | | 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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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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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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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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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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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
 | | 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
 | | 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
 | | 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
 | | 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
 | | 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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1AKL
 | | ALKALINE PROTEASE FROM PSEUDOMONAS AERUGINOSA IFO3080 | | Descriptor: | ALKALINE PROTEASE, CALCIUM ION, ZINC ION | | Authors: | Miyatake, H, Hata, Y, Fujii, T, Hamada, K, Morihara, K, Katsube, Y. | | Deposit date: | 1995-09-16 | | Release date: | 1996-03-08 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of the unliganded alkaline protease from Pseudomonas aeruginosa IFO3080 and its conformational changes on ligand binding.
J.Biochem.(Tokyo), 118, 1995
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1KDJ
 | | OXIDIZED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA | | Descriptor: | COPPER (II) ION, PLASTOCYANIN | | Authors: | Inoue, T, Gotowda, M, Hamada, K, Kohzuma, T, Yoshizaki, F, Sugimura, Y, Kai, Y. | | Deposit date: | 1998-05-08 | | Release date: | 1999-05-11 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | The structure and unusual pH dependence of plastocyanin from the fern Dryopteris crassirhizoma. The protonation of an active site histidine is hindered by pi-pi interactions.
J.Biol.Chem., 274, 1999
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3ALN
 | | Crystal Structure of human non-phosphorylated MKK4 kinase domain complexed with AMP-PNP | | Descriptor: | Dual specificity mitogen-activated protein kinase kinase 4, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Matsumoto, T, Kinoshita, T, Kirii, Y, Yokota, K, Hamada, K, Tada, T. | | Deposit date: | 2010-08-04 | | Release date: | 2010-10-27 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structures of MKK4 kinase domain reveal that substrate peptide binds to an allosteric site and induces an auto-inhibition state
Biochem.Biophys.Res.Commun., 400, 2010
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