3AUJ
 
 | | Structure of diol dehydratase complexed with glycerol | | Descriptor: | CALCIUM ION, COBALAMIN, Diol dehydrase alpha subunit, ... | | Authors: | Yamanishi, M, Kinoshita, K, Fukuoka, M, Shibata, T, Tobimatsu, T, Toraya, T. | | Deposit date: | 2011-02-07 | | Release date: | 2012-02-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols
Febs J., 279, 2012
|
|
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
|
|
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
|
|
2DEP
 | |
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
|
|
3WFZ
 | | Crystal structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase C236Y Mutant | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, Lacto-N-biose phosphorylase | | Authors: | Koyama, Y, Hidaka, M, Kawakami, M, Nishimoto, M, Kitaoka, M. | | Deposit date: | 2013-07-25 | | Release date: | 2013-10-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Directed evolution to enhance thermostability of galacto-N-biose/lacto-N-biose I phosphorylase.
Protein Eng.Des.Sel., 26, 2013
|
|
8XZ2
 | | The structural model of a homodimeric D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria | | Descriptor: | D-alanyl-D-alanine dipeptidase | | Authors: | Konuma, T, Takai, T, Tsuchiya, C, Nishida, M, Hashiba, M, Yamada, Y, Shirai, H, Motoda, Y, Nagadoi, A, Chikaishi, E, Akagi, K, Akashi, S, Yamazaki, T, Akutsu, H, Oe, A, Ikegami, T. | | Deposit date: | 2024-01-20 | | Release date: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria.
Protein Sci., 33, 2024
|
|
6IPW
 | | Crystal structure of CqsB2 from Streptomyces exfoliatus in complex with the product, 1-(2-hydroxypropyl)-2-methyl-carbazole-3,4-dione | | Descriptor: | 2-methyl-1-[(2R)-2-oxidanylpropyl]-9H-carbazole-3,4-dione, CqsB2 | | Authors: | Tomita, T, Kobayashi, M, Nishiyama, M, Kuzuyama, T. | | Deposit date: | 2018-11-05 | | Release date: | 2019-10-16 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces.
Angew.Chem.Int.Ed.Engl., 58, 2019
|
|
6IPV
 | |
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
|
|
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
|
|
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: | 2020-02-05 | | 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
|
|
3WWN
 | | Crystal structure of LysZ from Thermus thermophilus complex with LysW | | Descriptor: | OrfF, Putative acetylglutamate kinase-like protein, SULFATE ION, ... | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2014-06-21 | | Release date: | 2014-11-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
J.Biol.Chem., 290, 2015
|
|
3WWM
 | | Crystal structure of LysZ from Thermus thermophilus with ADP | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Putative acetylglutamate kinase-like protein | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2014-06-21 | | Release date: | 2014-11-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
J.Biol.Chem., 290, 2015
|
|
3WWL
 | | Crystal structure of lysine biosynthetic amino acid carrier protein LysW from Thermus thermophilus conjugated with alpha-aminoadipate | | Descriptor: | Alpha-aminoadipate carrier protein LysW, ZINC ION | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2014-06-21 | | Release date: | 2014-11-19 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
J.Biol.Chem., 290, 2015
|
|
8XI6
 | | SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab | | 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: | Ishimaru, H, Nishimura, M, Shigematsu, H, Marini, M.I, Hasegawa, N, Takamiya, R, Iwata, S, Mori, Y. | | Deposit date: | 2023-12-19 | | Release date: | 2024-04-24 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein.
J.Virol., 98, 2024
|
|
1JQD
 | | Crystal Structure Analysis of Human Histamine Methyltransferase (Thr105 Polymorphic Variant) Complexed with AdoHcy and Histamine | | Descriptor: | HISTAMINE, Histamine N-Methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Horton, J.R, Sawada, K, Nishibori, M, Zhang, X, Cheng, X. | | Deposit date: | 2001-08-06 | | Release date: | 2002-08-06 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.28 Å) | | Cite: | Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons.
Structure, 9, 2001
|
|
6ITD
 | | Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid | | Descriptor: | 3-(1-AMINOETHYL)NONANEDIOIC ACID, Slr0355 protein | | Authors: | Sakaki, K, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2018-11-21 | | Release date: | 2020-01-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Nat.Chem.Biol., 16, 2020
|
|
1Y7T
 | | Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Malate dehydrogenase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Tomita, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2004-12-10 | | Release date: | 2005-08-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H)
Biochem.Biophys.Res.Commun., 334, 2005
|
|
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: | 2023-11-22 | | 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
|
|
4Y1P
 | | Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus acidocaldarius complex with 3-isopropylmalate and Mg2+ | | Descriptor: | 3-ISOPROPYLMALIC ACID, 3-isopropylmalate dehydrogenase, MAGNESIUM ION, ... | | Authors: | Takahashi, K, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2015-02-08 | | Release date: | 2016-03-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Characterization of two beta-decarboxylating dehydrogenases from Sulfolobus acidocaldarius
Extremophiles, 20, 2016
|
|
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
|
|
8IP8
 | | Wheat 80S ribosome stalled on AUG-Stop boron dependently | | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein eL8, 40S ribosomal protein eS1, ... | | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | Deposit date: | 2023-03-14 | | Release date: | 2024-02-21 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
|
|
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
|
|
8IP9
 | | Wheat 40S ribosome in complex with a tRNAi | | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein S23, 40S ribosomal protein eS1, ... | | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | Deposit date: | 2023-03-14 | | Release date: | 2024-02-21 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
|
|
