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PDB: 58 results

1SRP
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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
5GUG
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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
8WM0
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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
1GC7
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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
1GC6
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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
7XZQ
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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
7XZR
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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
8JE4
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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
5XA0
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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
5XA1
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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
5X9Z
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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
1J19
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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
7VMW
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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
7VMY
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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
1UJB
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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
1UJC
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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
1UJ4
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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
1UJ6
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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
1UJ5
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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
1UKW
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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
256B
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IMPROVEMENT OF THE 2.5 ANGSTROMS RESOLUTION MODEL OF CYTOCHROME B562 BY REDETERMINING THE PRIMARY STRUCTURE AND USING MOLECULAR GRAPHICS
Descriptor: CYTOCHROME B562, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION
Authors:Hamada, K, Bethge, P.H, Mathews, F.S.
Deposit date:1990-01-16
Release date:1991-01-15
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Improvement of the 2.5 A resolution model of cytochrome b562 by redetermining the primary structure and using molecular graphics.
J.Mol.Biol., 148, 1981
8I06
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Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with CoA
Descriptor: COENZYME A, CYSTEINE, Serine acetyltransferase
Authors:Toyomoto, T, Ono, K, Shiba, T, Momitani, K, Zhang, T, Tsutsuki, H, Ishikawa, T, Hoso, K, Hamada, K, Rahman, A, Zhong, H, Akaike, T, Yamamoto, K, Matsuoka, M, Hanaoka, K, Niidome, T, Sawa, T.
Deposit date:2023-01-10
Release date:2023-11-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics.
Front Microbiol, 14, 2023
8I04
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Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with serine
Descriptor: PHOSPHATE ION, SERINE, Serine acetyltransferase
Authors:Toyomoto, T, Ono, K, Shiba, T, Momitani, K, Zhang, T, Tsutsuki, H, Ishikawa, T, Hoso, K, Hamada, K, Rahman, A, Zhong, H, Akaike, T, Yamamoto, K, Matsuoka, M, Hanaoka, K, Niidome, T, Sawa, T.
Deposit date:2023-01-10
Release date:2023-11-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics.
Front Microbiol, 14, 2023
8I09
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Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with butyl gallate
Descriptor: CYSTEINE, PHOSPHATE ION, Serine acetyltransferase, ...
Authors:Toyomoto, T, Ono, K, Shiba, T, Momitani, K, Zhang, T, Tsutsuki, H, Ishikawa, T, Hoso, K, Hamada, K, Rahman, A, Zhong, H, Akaike, T, Yamamoto, K, Matsuoka, M, Hanaoka, K, Niidome, T, Sawa, T.
Deposit date:2023-01-10
Release date:2023-11-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics.
Front Microbiol, 14, 2023
1AKL
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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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