1GCP
| CRYSTAL STRUCTURE OF VAV SH3 DOMAIN | Descriptor: | VAV PROTO-ONCOGENE | Authors: | Nishida, M, Nagata, K, Hachimori, Y, Ogura, K, Inagaki, F. | Deposit date: | 2000-08-08 | Release date: | 2001-08-08 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Novel recognition mode between Vav and Grb2 SH3 domains. EMBO J., 20, 2001
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1ZDX
| Solution Structure of the type 1 pilus assembly platform FimD(25-125) | Descriptor: | Outer membrane usher protein fimD | Authors: | Nishiyama, M, Horst, R, Herrmann, T, Vetsch, M, Bettendorff, P, Ignatov, O, Grutter, M, Wuthrich, K, Glockshuber, R, Capitani, G. | Deposit date: | 2005-04-15 | Release date: | 2005-06-14 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. Embo J., 24, 2005
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3VKW
| Crystal Structure of the Superfamily 1 Helicase from Tomato Mosaic Virus | Descriptor: | Replicase large subunit, SULFATE ION | Authors: | Nishikiori, M, Sugiyama, S, Xiang, H, Niiyama, M, Ishibashi, K, Inoue, T, Ishikawa, M, Matsumura, H, Katoh, E. | Deposit date: | 2011-11-22 | Release date: | 2012-07-11 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structure of the superfamily 1 helicase from tomato mosaic virus J.Virol., 86, 2012
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1WKI
| solution structure of ribosomal protein L16 from thermus thermophilus HB8 | Descriptor: | LSU ribosomal protein L16P | Authors: | Nishimura, M, Yoshida, T, Shirouzu, M, Terada, T, Kuramitsu, S, Yokoyama, S, Ohkubo, T, Kobayashi, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2004-05-31 | Release date: | 2004-12-14 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8 J.Mol.Biol., 344, 2004
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3A4U
| Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53 | Descriptor: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | Authors: | Nishio, M, Kamiya, Y, Mizushima, T, Wakatsuki, S, Sasakawa, H, Yamamoto, K, Uchiyama, S, Noda, M, McKay, A.R, Fukui, K, Hauri, H.P, Kato, K. | Deposit date: | 2009-07-17 | Release date: | 2010-01-05 | Last modified: | 2024-10-30 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency. Proc.Natl.Acad.Sci.USA, 107, 2010
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1X23
| Crystal structure of ubch5c | Descriptor: | Ubiquitin-conjugating enzyme E2 D3 | Authors: | Nakanishi, M, Teshima, N, Mizushima, T, Murata, S, Tanaka, K, Yamane, T. | Deposit date: | 2005-04-19 | Release date: | 2005-05-03 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystal structure of ubch5c To be Published
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1Q2H
| Phenylalanine Zipper Mediates APS Dimerization | Descriptor: | adaptor protein with pleckstrin homology and src homology 2 domains | Authors: | Dhe-Paganon, S, Werner, E.D, Nishi, M, Chi, Y.-I, Shoelson, S.E. | Deposit date: | 2003-07-24 | Release date: | 2004-08-03 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | A phenylalanine zipper mediates APS dimerization. Nat.Struct.Mol.Biol., 11, 2004
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1UC9
| Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, lysine biosynthesis enzyme | Authors: | Sakai, H, Vassylyeva, M.N, Matsuura, T, Sekine, S, Nishiyama, M, Terada, T, Shirouzu, M, Kuramitsu, S, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-04-09 | Release date: | 2003-09-23 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.38 Å) | Cite: | Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8 J.Mol.Biol., 332, 2003
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1UC8
| Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8 | Descriptor: | lysine biosynthesis enzyme | Authors: | Sakai, H, Vassylyeva, M.N, Matsuura, T, Sekine, S, Nishiyama, M, Terada, T, Shirouzu, M, Kuramitsu, S, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-04-09 | Release date: | 2003-09-23 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8 J.Mol.Biol., 332, 2003
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5WVO
| Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 | Descriptor: | DNA (cytosine-5)-methyltransferase 1, Histone H3.1, Ubiquitin, ... | Authors: | Ishiyama, S, Nishiyama, A, Nakanishi, M, Arita, K. | Deposit date: | 2016-12-28 | Release date: | 2017-11-15 | Last modified: | 2024-10-23 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance Mol. Cell, 68, 2017
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5B6Q
| Crystal structure of monomeric cytochrome c5 from Shewanella violacea | Descriptor: | HEME C, IMIDAZOLE, Soluble cytochrome cA | Authors: | Masanari, M, Fujii, S, Kawahara, K, Oki, H, Tsujino, H, Maruno, T, Kobayashi, Y, Ohkubo, T, Nishiyama, M, Harada, Y, Wakai, S, Sambongi, Y. | Deposit date: | 2016-06-01 | Release date: | 2016-10-19 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea Biosci.Biotechnol.Biochem., 2016
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8J3S
| Complex structure of human cytomegalovirus protease and a macrocyclic peptide ligand | Descriptor: | Assemblin, PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | Deposit date: | 2023-04-18 | Release date: | 2023-11-08 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.09 Å) | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases. Acs Med.Chem.Lett., 14, 2023
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8J3T
| Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand | Descriptor: | (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide, Assemblin | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | Deposit date: | 2023-04-18 | Release date: | 2023-11-08 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases. Acs Med.Chem.Lett., 14, 2023
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3AB4
| Crystal structure of feedback inhibition resistant mutant of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine | Descriptor: | Aspartokinase, LYSINE, THREONINE | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | Deposit date: | 2009-11-30 | Release date: | 2010-06-23 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.47 Å) | Cite: | Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum J.Biol.Chem., 285, 2010
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5XOY
| Crystal structure of LysK from Thermus thermophilus in complex with Lysine | Descriptor: | LYSINE, SULFATE ION, [LysW]-lysine hydrolase | Authors: | Tomita, T, Fujita, S, Hasebe, F, Cho, S.-H, Yoshida, A, Kuzuyama, T, Nishiyama, M. | Deposit date: | 2017-05-31 | Release date: | 2017-09-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.39 Å) | Cite: | Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW Biochem. Biophys. Res. Commun., 491, 2017
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3AH3
| Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution | Descriptor: | 1,2-ETHANEDIOL, Homoisocitrate dehydrogenase, SULFATE ION | Authors: | Tomita, T, Suzuki, Y, Kuzuyama, T, Nishiyama, M. | Deposit date: | 2010-04-13 | Release date: | 2011-02-02 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution Biochem.J., 431, 2010
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3AOE
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3AOG
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4WH2
| N-acetylhexosamine 1-kinase in complex with ADP | Descriptor: | ACETIC ACID, ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, ... | Authors: | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | Deposit date: | 2014-09-19 | Release date: | 2015-02-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.847 Å) | Cite: | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase Biochim.Biophys.Acta, 1854, 2015
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4WH1
| N-Acetylhexosamine 1-kinase (ligand free) | Descriptor: | ACETIC ACID, GLYCEROL, N-acetylhexosamine 1-kinase | Authors: | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | Deposit date: | 2014-09-19 | Release date: | 2015-02-11 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase Biochim.Biophys.Acta, 1854, 2015
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4WH3
| N-acetylhexosamine 1-kinase in complex with ATP | Descriptor: | ACETIC ACID, ADENOSINE-5'-TRIPHOSPHATE, GLYCEROL, ... | Authors: | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | Deposit date: | 2014-09-19 | Release date: | 2015-02-18 | Last modified: | 2024-10-30 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase Biochim.Biophys.Acta, 1854, 2015
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2DEP
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7YV1
| Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Isoform 2B of GTPase KRas, KA30L Fab H-chain, ... | Authors: | Irie, M, Fukami, T.A, Matsuo, A, Saka, K, Nishimura, M, Saito, H, Torizawa, T, Tanada, M, Ohta, A. | Deposit date: | 2022-08-18 | Release date: | 2023-07-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.454 Å) | Cite: | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. J.Am.Chem.Soc., 145, 2023
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6KTQ
| Crystal structure of catalytic domain of homocitrate synthase from Sulfolobus acidocaldarius (SaHCS(dRAM)) in complex with alpha-ketoglutarate/Zn2+/CoA | Descriptor: | 2-OXOGLUTARIC ACID, COENZYME A, Homocitrate synthase, ... | Authors: | Suzuki, T, Tomita, T, Kuzuyama, T, Nishiyama, M. | Deposit date: | 2019-08-28 | Release date: | 2020-09-02 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.98 Å) | Cite: | Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius. Febs J., 288, 2021
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2DT9
| Crystal structure of the regulatory subunit of aspartate kinase from Thermus flavus | Descriptor: | ACETATE ION, Aspartokinase, THREONINE | Authors: | Yoshida, A, Tomita, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | Deposit date: | 2006-07-11 | Release date: | 2007-07-17 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus Febs J., 276, 2009
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