3LQB
 
 | | Crystal structure of the hatching enzyme ZHE1 from the zebrafish Danio rerio | | Descriptor: | 1,2-ETHANEDIOL, LOC792177 protein, SULFATE ION, ... | | Authors: | Tanokura, M, Okada, A, Nagata, K, Yasumasu, S, Ohtsuka, J, Iuchi, I. | | Deposit date: | 2010-02-08 | | Release date: | 2010-09-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio
J.Mol.Biol., 402, 2010
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1J0T
 | | The solution structure of molt-inhibiting hormone from the kuruma prawn | | Descriptor: | MOLT-INHIBITING HORMONE | | Authors: | Katayama, H, Nagata, K, Ohira, T, Yumoto, F, Tanokura, M, Nagasawa, H. | | Deposit date: | 2002-11-22 | | Release date: | 2002-12-11 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | The solution structure of molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus
J.Biol.Chem., 278, 2003
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3GQB
 | | Crystal Structure of the A3B3 complex from V-ATPase | | Descriptor: | V-type ATP synthase alpha chain, V-type ATP synthase beta chain | | Authors: | Meher, M, Akimoto, S, Iwata, M, Nagata, K, Hori, Y, Yoshida, M, Yokoyama, S, Iwata, S, Yokoyama, K. | | Deposit date: | 2009-03-24 | | Release date: | 2009-11-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of A(3)B(3) complex of V-ATPase from Thermus thermophilus.
Embo J., 28, 2009
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4TMB
 | | CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 | | Descriptor: | FLAVIN MONONUCLEOTIDE, Old yellow enzyme | | Authors: | Horita, S, Kataoka, M, Kitamura, N, Nakagawa, T, Miyakawa, T, Ohtsuka, J, Nagata, K, Shimizu, S, Tanokura, M. | | Deposit date: | 2014-05-31 | | Release date: | 2015-02-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | An Engineered Old Yellow Enzyme that Enables Efficient Synthesis of (4R,6R)-Actinol in a One-Pot Reduction System
Chembiochem, 16, 2015
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4TMC
 | | CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 COMPLEXED with P-HYDROXYBENZALDEHYDE | | Descriptor: | FLAVIN MONONUCLEOTIDE, Old yellow enzyme, P-HYDROXYBENZALDEHYDE | | Authors: | Horita, S, Kataoka, M, Kitamura, N, Nakagawa, T, Miyakawa, T, Ohtsuka, J, Nagata, K, Shimizu, S, Tanokura, M. | | Deposit date: | 2014-05-31 | | Release date: | 2015-02-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | An Engineered Old Yellow Enzyme that Enables Efficient Synthesis of (4R,6R)-Actinol in a One-Pot Reduction System
Chembiochem, 16, 2015
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1WTB
 | | Complex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA | | Descriptor: | 5'-D(P*TP*AP*GP*G)-3', Heterogeneous nuclear ribonucleoprotein D0 | | Authors: | Enokizono, Y, Konishi, Y, Nagata, K, Ouhashi, K, Uesugi, S, Ishikawa, F, Katahira, M. | | Deposit date: | 2004-11-22 | | Release date: | 2005-04-05 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D
J.Biol.Chem., 280, 2005
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7VPY
 | | Crystal structure of the neutralizing nanobody P86 against SARS-CoV-2 | | Descriptor: | 1,2-ETHANEDIOL, Nanobody, SULFATE ION | | Authors: | Maeda, R, Fujita, J, Konishi, Y, Kazuma, Y, Yamazaki, H, Anzai, I, Yamaguchi, K, Kasai, K, Nagata, K, Yamaoka, Y, Miyakawa, K, Ryo, A, Shirakawa, K, Makino, F, Matsuura, Y, Inoue, T, Imura, A, Namba, K, Takaori-Kondo, A. | | Deposit date: | 2021-10-18 | | Release date: | 2022-07-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.
Commun Biol, 5, 2022
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7VQ0
 | | Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86 | | Descriptor: | 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Maeda, R, Fujita, J, Konishi, Y, Kazuma, Y, Yamazaki, H, Anzai, I, Yamaguchi, K, Kasai, K, Nagata, K, Yamaoka, Y, Miyakawa, K, Ryo, A, Shirakawa, K, Makino, F, Matsuura, Y, Inoue, T, Imura, A, Namba, K, Takaori-Kondo, A. | | Deposit date: | 2021-10-18 | | Release date: | 2022-07-20 | | Method: | ELECTRON MICROSCOPY (3.03 Å) | | Cite: | A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.
Commun Biol, 5, 2022
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2RQY
 | | Solution structure and dynamics of mouse ARMET | | Descriptor: | Putative uncharacterized protein | | Authors: | Hoseki, J, Sasakawa, H, Yamaguchi, Y, Maeda, M, Kubota, H, Kato, K, Nagata, K. | | Deposit date: | 2010-01-26 | | Release date: | 2010-04-21 | | Last modified: | 2022-03-16 | | Method: | SOLUTION NMR | | Cite: | Solution structure and dynamics of mouse ARMET.
Febs Lett., 584, 2010
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3A76
 | | The crystal structure of LinA | | Descriptor: | GLYCEROL, Gamma-hexachlorocyclohexane dehydrochlorinase, SPERMIDINE | | Authors: | Okai, M, Kubota, K, Fukuda, M, Nagata, Y, Nagata, K, Tanokura, M. | | Deposit date: | 2009-09-15 | | Release date: | 2010-09-15 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Crystal structure of g-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26
J.Mol.Biol., 2010
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2YYS
 | | Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8 | | Descriptor: | GLYCEROL, Proline iminopeptidase-related protein | | Authors: | Okai, M, Miyauchi, Y, Ebihara, A, Lee, W.C, Nagata, K, Tanokura, M. | | Deposit date: | 2007-05-01 | | Release date: | 2008-02-26 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8
Proteins, 70, 2008
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8WU8
 | | Crystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-RHINO(88-99) complex | | Descriptor: | Cell cycle checkpoint control protein RAD9A, Cell cycle checkpoint protein RAD1, Checkpoint protein HUS1, ... | | Authors: | Hara, K, Nagata, K, Iida, N, Hashimoto, H. | | Deposit date: | 2023-10-20 | | Release date: | 2024-02-14 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.81 Å) | | Cite: | Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO.
J.Biol.Chem., 300, 2024
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5B5I
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6AGZ
 | | Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542 | | Descriptor: | FLAVIN MONONUCLEOTIDE, Old Yellow Enzyme | | Authors: | Horita, S, Kataoka, M, Kitamura, N, Nakagawa, T, Miyakawa, T, Ohtsuka, J, Nagata, K, Shimizu, S, Tanokura, M. | | Deposit date: | 2018-08-15 | | Release date: | 2019-06-26 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 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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2KSW
 | | Backbone 1H, 13C, and 15N Chemical Shift Assignments for Oryctin | | Descriptor: | Oryctin | | Authors: | Horita, S, Ishibashi, J, Nagata, K, Miyakawa, T, Yamakawa, M, Tanokura, M. | | Deposit date: | 2010-01-14 | | Release date: | 2010-07-14 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | 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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2LDS
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7W3W
 | | X-ray structure of apo-VmFbpA, a ferric ion-binding protein from Vibrio metschnikovii | | Descriptor: | Iron-utilization periplasmic protein | | Authors: | Lu, P, Sui, M, Zhang, M, Nagata, K. | | Deposit date: | 2021-11-26 | | Release date: | 2021-12-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.858 Å) | | Cite: | Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake.
Int J Mol Sci, 22, 2021
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3EOQ
 | | The crystal structure of putative zinc protease beta-subunit from Thermus thermophilus HB8 | | Descriptor: | Putative zinc protease | | Authors: | Ohtsuka, J, Ichihara, Y, Ebihara, A, Yokoyama, S, Kuramitsu, S, Nagata, K, Tanokura, M. | | Deposit date: | 2008-09-29 | | Release date: | 2009-03-17 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | 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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8J4H
 | | X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with Danshensu (DSS) | | Descriptor: | (2~{R})-3-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-propanoic acid, Ferric iron ABC transporter iron-binding protein | | Authors: | Lu, P, Jiang, J, Nagata, K. | | Deposit date: | 2023-04-20 | | Release date: | 2024-01-10 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | 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 | | Descriptor: | CARBONATE ION, FE (III) ION, Ferric iron ABC transporter iron-binding protein | | Authors: | Lu, P, Jiang, J, Nagata, K. | | Deposit date: | 2023-04-20 | | Release date: | 2024-01-10 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | 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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1MKN
 | | N-TERMINAL HALF OF MIDKINE | | Descriptor: | PROTEIN (MIDKINE) | | Authors: | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | Deposit date: | 1999-03-16 | | Release date: | 1999-03-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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1MKC
 | | C-TERMINAL DOMAIN OF MIDKINE | | Descriptor: | PROTEIN (MIDKINE) | | Authors: | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | Deposit date: | 1999-03-16 | | Release date: | 1999-03-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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1K1Z
 | | Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav | | Descriptor: | vav | | Authors: | Ogura, K, Nagata, K, Horiuchi, M, Ebisui, E, Hasuda, T, Yuzawa, S, Nishida, M, Hatanaka, H, Inagaki, F. | | Deposit date: | 2001-09-26 | | Release date: | 2001-10-10 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | 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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8HYL
 | | Crystal structure of DO1 Fv-clasp fragment | | Descriptor: | VH-SARAH, VL-SARAH | | Authors: | Anan, Y, Lu, P, Nagata, K, Itakura, M, Uchida, K. | | Deposit date: | 2023-01-06 | | Release date: | 2024-02-14 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins.
Commun Biol, 7, 2024
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8J8T
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