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PDB: 101 件
5XIU
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Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin
分子名称: 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase RNF168, Ubiquitin-40S ribosomal protein S27a
著者Takahashi, T.S, Sato, Y, Fukai, S.
登録日2017-04-27
公開日2018-03-07
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Nat Commun, 9, 2018
5YJ9
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Crystal structure of Tribolium castaneum PINK1 kinase domain in complex with AMP-PNP
分子名称: MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Serine/threonine-protein kinase PINK1, ...
著者Okatsu, K, Sato, Y, Fukai, S.
登録日2017-10-09
公開日2018-07-25
実験手法X-RAY DIFFRACTION (2.53 Å)
主引用文献Structural insights into ubiquitin phosphorylation by PINK1.
Sci Rep, 8, 2018
3W1F
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Crystal structure of Human MPS1 catalytic domain in complex with 5-(5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl)-2-methylbenzenesulfonamide
分子名称: 5-[5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl]-2-methylbenzenesulfonamide, Dual specificity protein kinase TTK
著者Kusakabe, K, Ide, N, Daigo, Y, Tachibana, Y, Itoh, T, Yamamoto, T, Hashizume, H, Hato, Y, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Yasuo, K, Maeda, M, Higaki, M, Ueda, K, Yoshizawa, H, Baba, Y, Shiota, T, Murai, H, Nakamura, Y.
登録日2012-11-14
公開日2013-06-26
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Indazole-based potent and cell-active Mps1 kinase inhibitors: rational design from pan-kinase inhibitor anthrapyrazolone (SP600125)
J.Med.Chem., 56, 2013
5ZNM
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Colicin D Central Domain and C-terminal tRNase domain
分子名称: Colicin-D, GLYCEROL, SULFATE ION
著者Chang, J.W, Sato, Y, Ogawa, T, Arakawa, T, Fukai, S, Fushinobu, S, Masaki, H.
登録日2018-04-10
公開日2018-08-29
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell
J. Biochem., 164, 2018
3VQU
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-[(4-amino-5-cyano-6-ethoxypyridin-2- yl)amino]benzamide
分子名称: 4-[(4-amino-5-cyano-6-ethoxypyridin-2-yl)amino]benzamide, Dual specificity protein kinase TTK, IODIDE ION
著者Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Higashino, K, Okano, Y, Tadano, G, Tachibana, Y, Sato, Y, Inoue, M, Wada, T, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Tagashira, S, Kido, Y, Sakamoto, S, Yasuo, K, Maeda, M, Yamamoto, T, Higaki, M, Endoh, T, Ueda, K, Shiota, T, Murai, H, Nakamura, Y.
登録日2012-03-30
公開日2012-06-27
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Diaminopyridine-based potent and selective mps1 kinase inhibitors binding to an unusual flipped-Peptide conformation.
Acs Med.Chem.Lett., 3, 2012
3A58
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Crystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae
分子名称: Exocyst complex component SEC3, GTP-binding protein RHO1, MAGNESIUM ION, ...
著者Yamashita, M, Sato, Y, Yamagata, A, Mimura, H, Yoshikawa, A, Fukai, S.
登録日2009-08-03
公開日2010-01-12
最終更新日2021-11-10
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural basis for the Rho- and phosphoinositide-dependent localization of the exocyst subunit Sec3
Nat.Struct.Mol.Biol., 17, 2010
3WYY
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH (E)-3-(4-((6-(((3s,5s,7s)-adamantan-1-yl)amino)-4-amino-5-cyanopyridin-2-yl)amino)-2-(cyanomethoxy)phenyl)-N-(2-methoxyethyl)acrylamide
分子名称: (2E)-3-[4-({4-amino-5-cyano-6-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylamino]pyridin-2-yl}amino)-2-(cyanomethoxy)phenyl]-N-(2-methoxyethyl)prop-2-enamide, Dual specificity protein kinase TTK
著者Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Murai, H, Nakamura, Y.
登録日2014-09-10
公開日2015-04-08
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (3.05 Å)
主引用文献A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.
Bioorg.Med.Chem., 23, 2015
3WZJ
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-(6-(cyclohexylamino)-8-(((tetrahydro-2H-pyran-4-yl)methyl)amino)imidazo[1,2-b]pyridazin-3-yl)-N-cyclopropylbenzamide
分子名称: 4-{6-(cyclohexylamino)-8-[(tetrahydro-2H-pyran-4-ylmethyl)amino]imidazo[1,2-b]pyridazin-3-yl}-N-cyclopropylbenzamide, Dual specificity protein kinase TTK
著者Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y.
登録日2014-09-29
公開日2015-02-11
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献Discovery of imidazo[1,2-b]pyridazine derivatives: selective and orally available Mps1 (TTK) kinase inhibitors exhibiting remarkable antiproliferative activity.
J.Med.Chem., 58, 2015
3WYX
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 6-((3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-2-(cyclohexylamino)nicotinonitrile
分子名称: 6-{[3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl]amino}-2-(cyclohexylamino)pyridine-3-carbonitrile, Dual specificity protein kinase TTK, IODIDE ION
著者Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y.
登録日2014-09-09
公開日2015-04-08
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.
Bioorg.Med.Chem., 23, 2015
3WZK
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH N-cyclopropyl-4-(8-((thiophen-2-ylmethyl)amino)imidazo[1,2-a]pyrazin-3-yl)benzamide
分子名称: CHLORIDE ION, Dual specificity protein kinase TTK, N-cyclopropyl-4-{8-[(thiophen-2-ylmethyl)amino]imidazo[1,2-a]pyrazin-3-yl}benzamide
著者Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y.
登録日2014-09-29
公開日2015-02-11
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Discovery of imidazo[1,2-b]pyridazine derivatives: selective and orally available Mps1 (TTK) kinase inhibitors exhibiting remarkable antiproliferative activity.
J.Med.Chem., 58, 2015
5XWS
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Crystal structure of SALM5 LRR-Ig
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Leucine-rich repeat and fibronectin type-III domain-containing protein 5
著者Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S.
登録日2017-06-30
公開日2018-06-06
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (3.084 Å)
主引用文献Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Nat Commun, 9, 2018
5XWU
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Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S.
登録日2017-06-30
公開日2018-06-06
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (3.162 Å)
主引用文献Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Nat Commun, 9, 2018
5XWT
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Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S.
登録日2017-06-30
公開日2018-06-06
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (4.178 Å)
主引用文献Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Nat Commun, 9, 2018
3VDR
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Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)
分子名称: (3R)-3-hydroxybutanoic acid, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ACETOACETIC ACID, ...
著者Hoque, M.M, Shimizu, S, Juan, E.C.M, Sato, Y, Hossain, M.T, Yamamoto, T, Imamura, S, Amano, H, Suzuki, K, Sekiguchi, T, Tsunoda, M, Takenaka, A.
登録日2012-01-06
公開日2012-02-08
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
Acta Crystallogr.,Sect.F, 65, 2009
3A31
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Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix (selenomethionine derivative)
分子名称: Probable threonyl-tRNA synthetase 1, SULFATE ION, ZINC ION
著者Shimizu, S, Juan, E.C.M, Miyashita, Y, Sato, Y, Hoque, M.M, Suzuki, K, Yogiashi, M, Tsunoda, M, Dock-Bregeon, A.-C, Moras, D, Sekiguchi, T, Takenaka, A.
登録日2009-06-07
公開日2009-10-27
最終更新日2013-11-20
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain
J.Mol.Biol., 394, 2009
3A32
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Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix
分子名称: Probable threonyl-tRNA synthetase 1, SULFATE ION, ZINC ION
著者Shimizu, S, Juan, E.C.M, Miyashita, Y, Sato, Y, Hoque, M.M, Suzuki, K, Yogiashi, M, Tsunoda, M, Dock-Bregeon, A.-C, Moras, D, Sekiguchi, T, Takenaka, A.
登録日2009-06-07
公開日2009-10-27
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain
J.Mol.Biol., 394, 2009
3A36
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Structural insight into the membrane insertion of tail-anchored proteins by Get3
分子名称: ATPase GET3, ZINC ION
著者Yamagata, A, Mimura, H, Sato, Y, Yamashita, M, Yoshikawa, A, Fukai, S.
登録日2009-06-10
公開日2010-01-12
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Structural insight into the membrane insertion of tail-anchored proteins by Get3
Genes Cells, 15, 2010
3A1K
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Crystal structure of Rhodococcus sp. N771 Amidase
分子名称: Amidase
著者Ohtaki, A, Noguchi, K, Sato, Y, Murata, K, Odaka, M, Yohda, M.
登録日2009-04-09
公開日2009-11-03
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.17 Å)
主引用文献Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition
Biochim.Biophys.Acta, 1804, 2010
3A1I
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Crystal structure of Rhodococcus sp. N-771 Amidase complexed with Benzamide
分子名称: Amidase, BENZAMIDE
著者Ohtaki, A, Noguchi, K, Sato, Y, Murata, K, Odaka, M, Yohda, M.
登録日2009-04-03
公開日2009-10-27
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.32 Å)
主引用文献Structure and Characterization of Amidase from Rhodococcus sp. N-771: Insight into the Molecular Mechanism of Substrate Recognition
Biochim.Biophys.Acta, 2009
3A37
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Structural insight into the membrane insertion of tail-anchored proteins by Get3
分子名称: ADENOSINE-5'-DIPHOSPHATE, ATPase GET3, ZINC ION
著者Yamagata, A, Mimura, H, Sato, Y, Yamashita, M, Yoshikawa, A, Fukai, S.
登録日2009-06-10
公開日2010-01-12
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Structural insight into the membrane insertion of tail-anchored proteins by Get3
Genes Cells, 15, 2010
2Z6E
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BU of 2z6e by Molmil
Crystal Structure of Human DAAM1 FH2
分子名称: Disheveled-associated activator of morphogenesis 1
著者Yamashita, M, Higashi, T, Sato, Y, Shirakawa, R, Kita, T, Horiuchi, H, Fukai, S, Nureki, O.
登録日2007-07-31
公開日2008-05-27
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Crystal structure of human DAAM1 formin homology 2 domain
Genes Cells, 12, 2007
2E7S
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BU of 2e7s by Molmil
Crystal structure of the yeast Sec2p GEF domain
分子名称: Rab guanine nucleotide exchange factor SEC2
著者Fukai, S, Sato, Y, Nureki, O.
登録日2007-01-12
公開日2007-02-27
最終更新日2021-11-10
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Asymmetric Coiled-Coil Structure with Guanine Nucleotide Exchange Activity
Structure, 15, 2007
6J6X
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Crystal structure of apo GGTaseIII
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, Geranylgeranyl transferase type-2 subunit beta, MAGNESIUM ION, ...
著者Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S.
登録日2019-01-16
公開日2020-01-22
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.962 Å)
主引用文献Crystal structure of apo GGTaseIII
To Be Published
6J74
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Complex of GGTaseIII and full-length Ykt6
分子名称: Geranylgeranyl transferase type-2 subunit beta, PHOSPHATE ION, Protein prenyltransferase alpha subunit repeat-containing protein 1, ...
著者Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S.
登録日2019-01-16
公開日2020-01-22
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (3.212 Å)
主引用文献Complex of GGTaseIII and full-length Ykt6
To Be Published
6J7F
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Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP
分子名称: DIPHOSPHATE, FARNESYL, GERAN-8-YL GERAN, ...
著者Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S.
登録日2019-01-18
公開日2020-01-22
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.883 Å)
主引用文献Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP
To Be Published

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