7UPF
 
 | | Tau Paired Helical Filament from Alzheimer's Disease incubated 1 hr. with EGCG | | Descriptor: | Isoform Tau-F of Microtubule-associated protein tau | | Authors: | Seidler, P.M, Murray, K.A, Boyer, D.R, Ge, P, Sawaya, M.R, Eisenberg, D.S. | | Deposit date: | 2022-04-15 | | Release date: | 2022-09-28 | | Last modified: | 2024-06-12 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structure-based discovery of small molecules that disaggregate Alzheimer's disease tissue derived tau fibrils in vitro.
Nat Commun, 13, 2022
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5Y80
 | | Complex structure of cyclin G-associated kinase with gefitinib | | Descriptor: | Cyclin-G-associated kinase, Gefitinib, NANOBODY | | Authors: | Ohbayashi, N, Murayama, K, Kato-Murayama, M, Shirouzu, M. | | Deposit date: | 2017-08-18 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib.
ChemistryOpen, 7, 2018
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8WTQ
 | | HUMAN SQUALENE SYNTHASE IN COMPLEX WITH {1-[2-Chloro-5-(2,2-dimethyl-propyl)-13-(2-methoxy-phenyl)-6-oxo-6,7,10,11-tetrahydro-5H,9H,13H-12-oxa-5,8-diaza-benzocycloundecene-8-carbonyl]-piperidin-4-yl}-acetic acid | | Descriptor: | 2-[1-[[(10~{S})-13-chloranyl-2-(2,2-dimethylpropyl)-10-(2-methoxyphenyl)-3-oxidanylidene-9-oxa-2,5-diazabicyclo[9.4.0]pentadeca-1(15),11,13-trien-5-yl]carbonyl]piperidin-4-yl]ethanoic acid, PHOSPHATE ION, Squalene synthase | | Authors: | Suzuki, M, Haginoya, N, Suzuki, M, Ishigai, Y, Terayama, K, Kanda, A, Sugita, K. | | Deposit date: | 2023-10-19 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Discovery of Novel 11-Membered Templates as Squalene Synthase Inhibitors.
J.Med.Chem., 67, 2024
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8WTR
 | | HUMAN SQUALENE SYNTHASE IN COMPLEX WITH (1S,3R)-3-[2-Chloro-5-(2,2-dimethyl-propyl)-13-(2-methoxy-phenyl)-6,8-dioxo-5,6,7,8,10,11-hexahydro-13H-12-oxa-5,9-diaza-benzocycloundecen-9-yl]-cyclohexanecarboxylic acid | | Descriptor: | (1~{S},3~{R})-3-[(10~{S})-13-chloranyl-2-(2,2-dimethylpropyl)-10-(2-methoxyphenyl)-3,5-bis(oxidanylidene)-9-oxa-2,6-diazabicyclo[9.4.0]pentadeca-1(15),11,13-trien-6-yl]cyclohexane-1-carboxylic acid, PHOSPHATE ION, Squalene synthase | | Authors: | Suzuki, M, Haginoya, N, Suzuki, M, Ishigai, Y, Terayama, K, Kanda, A, Sugita, K. | | Deposit date: | 2023-10-19 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Discovery of Novel 11-Membered Templates as Squalene Synthase Inhibitors.
J.Med.Chem., 67, 2024
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2CWK
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2DXF
 | | Crystal structure of nucleoside diphosphate kinase in complex with GTP analog | | Descriptor: | CHLORIDE ION, Nucleoside diphosphate kinase, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Kato-Murayama, M, Murayama, K, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-08-25 | | Release date: | 2007-02-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structure of nucleoside diphosphate kinase in complex with GTP analog
To be Published
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2DXA
 | | Crystal structure of trans editing enzyme ProX from E.coli | | Descriptor: | CHLORIDE ION, Protein ybaK | | Authors: | Kato-Murayama, M, Murayama, K, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-08-25 | | Release date: | 2007-02-25 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Crystal structure of trans editing enzyme ProX from E.coli
To be Published
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2DYC
 | | Crystal structure of the N-terminal domain of mouse galectin-4 | | Descriptor: | Galectin-4 | | Authors: | Kato-Murayama, M, Murayama, K, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-09-08 | | Release date: | 2007-10-16 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of the N-terminal domain of mouse galectin-4
To be Published
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2DXD
 | | Crystal structure of nucleoside diphosphate kinase in complex with ATP analog | | Descriptor: | ADENOSINE MONOPHOSPHATE, CHLORIDE ION, Nucleoside diphosphate kinase | | Authors: | Kato-Murayama, M, Murayama, K, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-08-25 | | Release date: | 2007-02-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Crystal structure of nucleoside diphosphate kinase in complex with ATP analog
To be Published
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2DXE
 | | Crystal structure of nucleoside diphosphate kinase in complex with GDP | | Descriptor: | CHLORIDE ION, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Kato-Murayama, M, Murayama, K, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-08-25 | | Release date: | 2007-02-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structure of nucleoside diphosphate kinase in complex with GDP
To be Published
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1WXX
 | | Crystal structure of Tt1595, a putative SAM-dependent methyltransferase from Thermus thermophillus HB8 | | Descriptor: | PHOSPHATE ION, POTASSIUM ION, hypothetical protein TTHA1280 | | Authors: | Pioszak, A.A, Murayama, K, Nakagawa, N, Ebihara, A, Kuramitsu, S, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-02-02 | | Release date: | 2005-08-02 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine.
Acta Crystallogr.,Sect.F, 61, 2005
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7JKV
 | | Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420 | | Descriptor: | 3C-like proteinase, N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, PENTAETHYLENE GLYCOL | | Authors: | Bulut, H, Hattori, S.I, Das, D, Murayama, K, Mitsuya, H. | | Deposit date: | 2020-07-29 | | Release date: | 2020-09-23 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.
Nat Commun, 12, 2021
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7YM0
 | | Lysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+ | | Descriptor: | CALCIUM ION, Lysoplasmalogenase | | Authors: | Yasutake, Y, Sakasegawa, S, Sugimori, D, Murayama, K. | | Deposit date: | 2022-07-27 | | Release date: | 2023-01-04 | | Method: | X-RAY DIFFRACTION (2.91 Å) | | Cite: | Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668.
Biosci.Biotechnol.Biochem., 87, 2022
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2PSM
 | | Crystal structure of Interleukin 15 in complex with Interleukin 15 receptor alpha | | Descriptor: | BENZAMIDINE, Interleukin-15, Interleukin-15 receptor alpha chain | | Authors: | Olsen, S.K, Murayama, K, Kishishita, S, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Ota, N, Kanagawa, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-05-07 | | Release date: | 2007-11-06 | | Last modified: | 2021-08-18 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Crystal Structure of the Interleukin-15{middle dot}Interleukin-15 Receptor {alpha} Complex: INSIGHTS INTO TRANS AND CIS PRESENTATION
J.Biol.Chem., 282, 2007
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2ZCC
 | | Ubiquitin crystallized under high pressure | | Descriptor: | Ubiquitin, ZINC ION | | Authors: | Kitahara, R, Tanaka, T, Yamashita, M, Araya, K, Yokoyama, S, Akasaka, K, Taniguchi, Y, Kato, M. | | Deposit date: | 2007-11-08 | | Release date: | 2007-11-20 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structure of Ubiquitin crystallized under high pressure
to be published
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6LP1
 | | Crystal structure of acetate:succinate CoA transferase (ASCT) from Trypanosoma brucei. | | Descriptor: | CALCIUM ION, GLYCEROL, Succinyl-CoA:3-ketoacid-coenzyme A transferase | | Authors: | Mochizuki, K, Inaoka, D.K, Shiba, T, Fukuda, K, Kurasawa, H, Mazet, M, Millerioux, Y, Bringaud, F, Boshart, M, Balogun, E.O, Harada, S, Hirayama, K, Kita, K. | | Deposit date: | 2020-01-08 | | Release date: | 2020-10-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | The ASCT/SCS cycle fuels mitochondrial ATP and acetate production in Trypanosoma brucei.
Biochim Biophys Acta Bioenerg, 1861, 2020
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2CZL
 | | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol) | | Descriptor: | 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL, L(+)-TARTARIC ACID, POTASSIUM ION, ... | | Authors: | Arai, R, Nishino, A, Nagano, K, Kamo-Uchikubo, T, Nishimoto, M, Toyama, M, Terada, T, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-13 | | Release date: | 2006-01-13 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
J.Struct.Biol., 168, 2009
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3A3U
 | | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 | | Descriptor: | 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL, L(+)-TARTARIC ACID, Menaquinone biosynthetic enzyme, ... | | Authors: | Arai, R, Nishino, A, Nagano, K, Uchikubo-Kamo, T, Katsura, K, Nishimoto, M, Toyama, M, Terada, T, Kuramitsu, S, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-06-20 | | Release date: | 2009-07-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
J.Struct.Biol., 168, 2009
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2CZJ
 | | Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8 | | Descriptor: | SsrA-binding protein, tmRNA (63-MER) | | Authors: | Bessho, Y, Shibata, R, Sekine, S, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-13 | | Release date: | 2006-10-31 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3.01 Å) | | Cite: | Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Proc.Natl.Acad.Sci.Usa, 104, 2007
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2CWJ
 | | crystal structure of APE1501, a putative endonuclease from Aeropyrum pernix | | Descriptor: | putative endonuclease | | Authors: | Takemoto-hori, C, Suetsugu-hanawa, K, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-06-21 | | Release date: | 2005-12-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | crystal structure of APE1501, a putative endonuclease from Aeropyrum pernix
To be Published
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2Z0W
 | | Crystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a swapped-dimer | | Descriptor: | CAP-Gly domain-containing linker protein 4 | | Authors: | Saito, K, Yoshikawa, S, Nishino, A, Murayama, K, Terada, T, Shirouzu, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-05-07 | | Release date: | 2007-11-13 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a swapped-dimer
To be Published
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2Z13
 | | Crystal structure of the N-terminal DUF1126 in human EF-hand domain | | Descriptor: | EF-hand domain-containing family member C2 | | Authors: | Saito, K, Kishishita, S, Nishino, A, Murayama, K, Terada, T, Shirouzu, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-05-07 | | Release date: | 2007-11-13 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Crystal structure of the N-terminal DUF1126 in human EF-hand domain
To be Published
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2Z15
 | | Crystal structure of human Tob1 protein | | Descriptor: | Protein Tob1 | | Authors: | Saito, K, Kishishita, S, Nishino, A, Murayama, K, Terada, T, Shirouzu, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-05-08 | | Release date: | 2007-11-13 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of human Tob1 protein
To be Published
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3WJJ
 | | Crystal structure of IIb selective Fc variant, Fc(P238D), in complex with FcgRIIb | | Descriptor: | Ig gamma-1 chain C region, Low affinity immunoglobulin gamma Fc region receptor II-b, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Kadono, S, Mimoto, F, Katada, H, Igawa, T, Kuramochi, T, Muraoka, M, Wada, Y, Haraya, K, Miyazaki, T, Hattori, K. | | Deposit date: | 2013-10-10 | | Release date: | 2013-11-13 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Engineered antibody Fc variant with selectively enhanced Fc gamma RIIb binding over both Fc gamma RIIaR131 and Fc gamma RIIaH131.
Protein Eng.Des.Sel., 26, 2013
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2DUK
 | | Crystal structure of MS0616 | | Descriptor: | MS0616 | | Authors: | Hosaka, T, Nishino, A, Uchikubo, K.-T, Kishishita, S, Murayama, K, Shirouzu, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-07-24 | | Release date: | 2007-01-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.62 Å) | | Cite: | Crystal structure of MS0616
To be Published
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