1MKN
 
 | | N-TERMINAL HALF OF MIDKINE | | 分子名称: | PROTEIN (MIDKINE) | | 著者 | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | 登録日 | 1999-03-16 | | 公開日 | 1999-03-23 | | 最終更新日 | 2023-12-27 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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1MKC
 | | C-TERMINAL DOMAIN OF MIDKINE | | 分子名称: | PROTEIN (MIDKINE) | | 著者 | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | 登録日 | 1999-03-16 | | 公開日 | 1999-03-23 | | 最終更新日 | 2024-11-06 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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3ZFK
 | | N-terminal truncated Nuclease Domain of Colicin E7 | | 分子名称: | ACETATE ION, CHLORIDE ION, COLICIN-E7, ... | | 著者 | Toth, E, Czene, A, Gyurcsik, B, Otten, H, Poulsen, J.-C.N, Larsen, S, Christensen, H.E.M, Nagata, K. | | 登録日 | 2012-12-11 | | 公開日 | 2013-12-18 | | 最終更新日 | 2023-12-20 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | A New Insight Into the Zinc-Dependent DNA-Cleavage by the Colicin E7 Nuclease: A Crystallographic and Computational Study.
Metallomics, 6, 2014
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8K4R
 | | Structure of VinM-VinL complex | | 分子名称: | Acyl-carrier-protein, Non-ribosomal peptide synthetase, SODIUM ION, ... | | 著者 | Miyanaga, A, Nagata, K, Nakajima, J, Chisuga, T, Kudo, F, Eguchi, T. | | 登録日 | 2023-07-20 | | 公開日 | 2023-11-01 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Structural Basis of Amide-Forming Adenylation Enzyme VinM in Vicenistatin Biosynthesis.
Acs Chem.Biol., 18, 2023
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4IJ5
 | | Crystal Structure of a Novel-type Phosphoserine Phosphatase from Hydrogenobacter thermophilus TK-6 | | 分子名称: | 1,2-ETHANEDIOL, CHLORIDE ION, Phosphoserine phosphatase 1 | | 著者 | Chiba, Y, Horita, S, Ohtsuka, J, Arai, H, Nagata, K, Igarashi, Y, Tanokura, M, Ishii, M. | | 登録日 | 2012-12-21 | | 公開日 | 2013-03-20 | | 最終更新日 | 2024-10-09 | | 実験手法 | X-RAY DIFFRACTION (1.5 Å) | | 主引用文献 | Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis
J.Biol.Chem., 288, 2013
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8HYL
 | | Crystal structure of DO1 Fv-clasp fragment | | 分子名称: | VH-SARAH, VL-SARAH | | 著者 | Anan, Y, Lu, P, Nagata, K, Itakura, M, Uchida, K. | | 登録日 | 2023-01-06 | | 公開日 | 2024-02-14 | | 最終更新日 | 2024-10-30 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins.
Commun Biol, 7, 2024
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6AGZ
 | | Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542 | | 分子名称: | FLAVIN MONONUCLEOTIDE, Old Yellow Enzyme | | 著者 | Horita, S, Kataoka, M, Kitamura, N, Nakagawa, T, Miyakawa, T, Ohtsuka, J, Nagata, K, Shimizu, S, Tanokura, M. | | 登録日 | 2018-08-15 | | 公開日 | 2019-06-26 | | 最終更新日 | 2024-03-27 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds.
Biosci.Biotechnol.Biochem., 83, 2019
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3D79
 | | Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3 | | 分子名称: | Putative uncharacterized protein PH0734 | | 著者 | Nishimura, Y, Miyazono, K, Sawano, Y, Makino, T, Nagata, K, Tanokura, M. | | 登録日 | 2008-05-20 | | 公開日 | 2008-12-09 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (1.73 Å) | | 主引用文献 | Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3.
Proteins, 73, 2008
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2RQY
 | | Solution structure and dynamics of mouse ARMET | | 分子名称: | Putative uncharacterized protein | | 著者 | Hoseki, J, Sasakawa, H, Yamaguchi, Y, Maeda, M, Kubota, H, Kato, K, Nagata, K. | | 登録日 | 2010-01-26 | | 公開日 | 2010-04-21 | | 最終更新日 | 2024-11-06 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Solution structure and dynamics of mouse ARMET.
Febs Lett., 584, 2010
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8J4H
 | | X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with Danshensu (DSS) | | 分子名称: | (2~{R})-3-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-propanoic acid, Ferric iron ABC transporter iron-binding protein | | 著者 | Lu, P, Jiang, J, Nagata, K. | | 登録日 | 2023-04-20 | | 公開日 | 2024-01-10 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (2.01 Å) | | 主引用文献 | Molecular mechanism of Fe 3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu.
Protein Sci., 33, 2024
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8J4J
 | | X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with ferric ion | | 分子名称: | CARBONATE ION, FE (III) ION, Ferric iron ABC transporter iron-binding protein | | 著者 | Lu, P, Jiang, J, Nagata, K. | | 登録日 | 2023-04-20 | | 公開日 | 2024-01-10 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (2.15 Å) | | 主引用文献 | Molecular mechanism of Fe 3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu.
Protein Sci., 33, 2024
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1R5Z
 | | Crystal Structure of Subunit C of V-ATPase | | 分子名称: | V-type ATP synthase subunit C | | 著者 | Iwata, M, Imamura, H, Stambouli, E, Ikeda, C, Tamakoshi, M, Nagata, K, Makyio, H, Hankamer, B, Barber, J, Yoshida, M, Yokoyama, K, Iwata, S. | | 登録日 | 2003-10-14 | | 公開日 | 2004-01-13 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (1.95 Å) | | 主引用文献 | Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase.
Proc.Natl.Acad.Sci.Usa, 101, 2004
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3EOQ
 | | The crystal structure of putative zinc protease beta-subunit from Thermus thermophilus HB8 | | 分子名称: | Putative zinc protease | | 著者 | Ohtsuka, J, Ichihara, Y, Ebihara, A, Yokoyama, S, Kuramitsu, S, Nagata, K, Tanokura, M. | | 登録日 | 2008-09-29 | | 公開日 | 2009-03-17 | | 最終更新日 | 2024-10-09 | | 実験手法 | X-RAY DIFFRACTION (2.29 Å) | | 主引用文献 | Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase.
Proteins, 2009
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2EB1
 | | Crystal Structure of the C-Terminal RNase III Domain of Human Dicer | | 分子名称: | Endoribonuclease Dicer, MAGNESIUM ION | | 著者 | Takeshita, D, Zenno, S, Lee, W.C, Nagata, K, Saigo, K, Tanokura, M. | | 登録日 | 2007-02-05 | | 公開日 | 2007-11-06 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Homodimeric Structure and Double-stranded RNA Cleavage Activity of the C-terminal RNase III Domain of Human Dicer
J.Mol.Biol., 374, 2007
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4H8N
 | | Crystal structure of conjugated polyketone reductase C2 from candida parapsilosis complexed with NADPH | | 分子名称: | Conjugated polyketone reductase C2, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | 著者 | Qin, H.-M, Yamamura, A, Miyakawa, T, Maruoka, S, Ohtsuka, J, Nagata, K, Kataoka, M, Shimizu, S, Tanokura, M. | | 登録日 | 2012-09-23 | | 公開日 | 2013-08-07 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Structure of conjugated polyketone reductase from Candida parapsilosis IFO 0708 reveals conformational changes for substrate recognition upon NADPH binding
Appl.Microbiol.Biotechnol., 98, 2014
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1IX5
 | | Solution structure of the Methanococcus thermolithotrophicus FKBP | | 分子名称: | FKBP | | 著者 | Suzuki, R, Nagata, K, Kawakami, M, Nemoto, N, Furutani, M, Adachi, K, Maruyama, T, Tanokura, M. | | 登録日 | 2002-06-12 | | 公開日 | 2003-06-10 | | 最終更新日 | 2023-12-27 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Three-dimensional Solution Structure of an Archaeal FKBP with a Dual Function of Peptidyl Prolyl cis-trans Isomerase and Chaperone-like Activities
J.MOL.BIOL., 328, 2003
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1GCQ
 | | CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS | | 分子名称: | (4R)-2-METHYLPENTANE-2,4-DIOL, GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2, VAV PROTO-ONCOGENE | | 著者 | Nishida, M, Nagata, K, Hachimori, Y, Ogura, K, Inagaki, F. | | 登録日 | 2000-08-08 | | 公開日 | 2001-08-08 | | 最終更新日 | 2023-12-27 | | 実験手法 | X-RAY DIFFRACTION (1.68 Å) | | 主引用文献 | Novel recognition mode between Vav and Grb2 SH3 domains.
EMBO J., 20, 2001
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2KSW
 | | Backbone 1H, 13C, and 15N Chemical Shift Assignments for Oryctin | | 分子名称: | Oryctin | | 著者 | Horita, S, Ishibashi, J, Nagata, K, Miyakawa, T, Yamakawa, M, Tanokura, M. | | 登録日 | 2010-01-14 | | 公開日 | 2010-07-14 | | 最終更新日 | 2023-06-14 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Isolation, cDNA cloning, and structure-based functional characterization of oryctin, a hemolymph protein from the coconut rhinoceros beetle, Oryctes rhinoceros, as a novel serine protease inhibitor
J.Biol.Chem., 285, 2010
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8J8D
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8J8T
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1GCP
 | | CRYSTAL STRUCTURE OF VAV SH3 DOMAIN | | 分子名称: | VAV PROTO-ONCOGENE | | 著者 | Nishida, M, Nagata, K, Hachimori, Y, Ogura, K, Inagaki, F. | | 登録日 | 2000-08-08 | | 公開日 | 2001-08-08 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Novel recognition mode between Vav and Grb2 SH3 domains.
EMBO J., 20, 2001
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1K1Z
 | | Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav | | 分子名称: | vav | | 著者 | Ogura, K, Nagata, K, Horiuchi, M, Ebisui, E, Hasuda, T, Yuzawa, S, Nishida, M, Hatanaka, H, Inagaki, F. | | 登録日 | 2001-09-26 | | 公開日 | 2001-10-10 | | 最終更新日 | 2024-05-29 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Solution structure of N-terminal SH3 domain of Vav and the recognition site for Grb2 C-terminal SH3 domain
J.BIOMOL.NMR, 22, 2002
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2D37
 | | The Crystal Structure of Flavin Reductase HpaC complexed with NAD+ | | 分子名称: | FLAVIN MONONUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, hypothetical NADH-dependent FMN oxidoreductase | | 著者 | Okai, M, Kudo, N, Lee, W.C, Kamo, M, Nagata, K, Tanokura, M. | | 登録日 | 2005-09-26 | | 公開日 | 2006-05-30 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Biochemistry, 45, 2006
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2D7J
 | | Crystal Structure Analysis of Glutamine Amidotransferase from Pyrococcus horikoshii OT3 | | 分子名称: | GMP synthase [glutamine-hydrolyzing] subunit A | | 著者 | Maruoka, S, Lee, W.C, Kamo, M, Kudo, N, Nagata, K, Tanokura, M. | | 登録日 | 2005-11-21 | | 公開日 | 2006-11-21 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.89 Å) | | 主引用文献 | Crystal structure of glutamine amidotransferase from Pyrococcus horikoshii OT3
PROC.JPN.ACAD.,SER.B, 81, 2005
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2EGD
 | | Crystal structure of human S100A13 in the Ca2+-bound state | | 分子名称: | CALCIUM ION, Protein S100-A13 | | 著者 | Imai, F.L, Nagata, K, Yonezawa, N, Nakano, M, Tanokura, M. | | 登録日 | 2007-02-28 | | 公開日 | 2008-03-11 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (1.8 Å) | | 主引用文献 | Crystal structure of human S100A13 in the Ca2+-bound state
Acta Crystallogr.,Sect.F, 64, 2008
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