1UDY
 
 | | Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA | | Descriptor: | 3-THIAOCTANOYL-COENZYME A, Acyl-CoA dehydrogenase, medium-chain specific, ... | | Authors: | Satoh, A, Nakajima, Y, Miyahara, I, Hirotsu, K, Tanaka, T, Nishina, Y, Shiga, K, Tamaoki, H, Setoyama, C, Miura, R. | | Deposit date: | 2003-05-07 | | Release date: | 2003-12-09 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
J.BIOCHEM.(TOKYO), 134, 2003
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5IJA
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7CMN
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5AYV
 | | Crystal structure of archaeal ketopantoate reductase complexed with coenzyme A and 2-oxopantoate | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-dehydropantoate 2-reductase, ACETATE ION, ... | | Authors: | Aikawa, Y, Nishitani, Y, Miki, K. | | Deposit date: | 2015-09-08 | | Release date: | 2016-01-27 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.647 Å) | | Cite: | Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2-oxopantoate provides structural insights into feedback regulation
Proteins, 84, 2016
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1PRU
 | | PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING | | Descriptor: | PURINE REPRESSOR | | Authors: | Nagadoi, A, Morikawa, S, Nakamura, H, Enari, M, Kobayashi, K, Yamamoto, H, Sampei, G, Mizobuchi, K, Schumacher, M.A, Brennan, R.G, Nishimura, Y. | | Deposit date: | 1995-05-08 | | Release date: | 1996-03-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.
Structure, 3, 1995
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1PRV
 | | PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING | | Descriptor: | PURINE REPRESSOR | | Authors: | Nagadoi, A, Morikawa, S, Nakamura, H, Enari, M, Kobayashi, K, Yamamoto, H, Sampei, G, Mizobuchi, K, Schumacher, M.A, Brennan, R.G, Nishimura, Y. | | Deposit date: | 1995-05-08 | | Release date: | 1996-03-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.
Structure, 3, 1995
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7FBO
 | | geranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BezA, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Tsutsumi, H, Moriwaki, Y, Terada, T, Shimizu, K, Katsuyama, Y, Ohnishi, Y. | | Deposit date: | 2021-07-12 | | Release date: | 2021-12-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase.
Angew.Chem.Int.Ed.Engl., 61, 2022
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1MHW
 | | Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides | | Descriptor: | 4-biphenylacetyl-Cys-(D)Arg-Tyr-N-(2-phenylethyl) amide, Cathepsin L | | Authors: | Chowdhury, S, Sivaraman, J, Wang, J, Devanathan, G, Lachance, P, Qi, H, Menard, R, Lefebvre, J, Konishi, Y, Cygler, M, Sulea, T, Purisima, E.O. | | Deposit date: | 2002-08-21 | | Release date: | 2002-12-11 | | Last modified: | 2017-10-11 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides
J.Med.Chem., 45, 2002
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1EVI
 | | THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE | | Descriptor: | 3,4-DIHYDRO-2H-PYRROLIUM-5-CARBOXYLATE, D-AMINO ACID OXIDASE, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Mizutani, H, Miyahara, I, Hirotsu, K, Nishina, Y, Shiga, K, Setoyama, C, Miura, R. | | Deposit date: | 2000-04-20 | | Release date: | 2000-10-23 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin.
J.Biochem.(Tokyo), 128, 2000
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1BHI
 | | STRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STRUCTURES | | Descriptor: | CRE-BP1 | | Authors: | Nagadoi, A, Nakazawa, K, Uda, H, Maekawa, T, Ishii, S, Nishimura, Y. | | Deposit date: | 1998-06-09 | | Release date: | 1999-06-15 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain.
J.Mol.Biol., 287, 1999
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1FEX
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2ZK7
 | | Structure of a C-terminal deletion mutant of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) | | Descriptor: | Glucose 1-dehydrogenase related protein | | Authors: | Nishioka, T, Yasutake, Y, Nishiya, Y, Tamura, N, Tamura, T. | | Deposit date: | 2008-03-12 | | Release date: | 2009-01-13 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.71 Å) | | Cite: | C-terminal tail derived from the neighboring subunit is critical for the activity of Thermoplasma acidophilum D-aldohexose dehydrogenase
Proteins, 74, 2009
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3AUU
 | | Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with D-glucose | | Descriptor: | Glucose 1-dehydrogenase 4, beta-D-glucopyranose | | Authors: | Nishioka, T, Yasutake, Y, Nishiya, Y, Tamura, T. | | Deposit date: | 2011-02-16 | | Release date: | 2012-02-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV
Febs J., 279, 2012
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3AUS
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3AUT
 | | Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with NADH | | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Glucose 1-dehydrogenase 4 | | Authors: | Nishioka, T, Yasutake, Y, Nishiya, Y, Tamura, T. | | Deposit date: | 2011-02-16 | | Release date: | 2012-02-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV
Febs J., 279, 2012
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3AY6
 | | Crystal structure of Bacillus megaterium glucose dehydrogenase 4 A258F mutant in complex with NADH and D-glucose | | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, CHLORIDE ION, Glucose 1-dehydrogenase 4, ... | | Authors: | Nishioka, T, Yasutake, Y, Nishiya, Y, Tamura, T. | | Deposit date: | 2011-04-29 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV
Febs J., 279, 2012
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3AY7
 | | Crystal structure of Bacillus megaterium glucose dehydrogenase 4 G259A mutant | | Descriptor: | CHLORIDE ION, Glucose 1-dehydrogenase 4 | | Authors: | Nishioka, T, Yasutake, Y, Nishiya, Y, Tamura, T. | | Deposit date: | 2011-04-29 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV
Febs J., 279, 2012
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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: | 2024-10-30 | | 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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1Y1C
 | | Solution structure of Anemonia elastase inhibitor analogue | | Descriptor: | Elastase inhibitor | | Authors: | Hemmi, H, Kumazaki, T, Yoshizawa-Kumagaye, K, Nishiuchi, Y, Yoshida, T, Ohkubo, T, Kobayashi, Y. | | Deposit date: | 2004-11-18 | | Release date: | 2005-07-19 | | Last modified: | 2024-10-16 | | Method: | SOLUTION NMR | | Cite: | Structural and Functional Study of an Anemonia Elastase Inhibitor, a "Nonclassical" Kazal-Type Inhibitor from Anemonia sulcata
Biochemistry, 44, 2005
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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 | | Last modified: | 2024-10-23 | | 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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1Y1B
 | | Solution structure of Anemonia elastase inhibitor | | Descriptor: | Elastase inhibitor | | Authors: | Hemmi, H, Kumazaki, T, Yoshizawa-Kumagaye, K, Nishiuchi, Y, Yoshida, T, Ohkubo, T, Kobayashi, Y. | | Deposit date: | 2004-11-18 | | Release date: | 2005-07-19 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | Structural and Functional Study of an Anemonia Elastase Inhibitor, a "Nonclassical" Kazal-Type Inhibitor from Anemonia sulcata
Biochemistry, 44, 2005
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5XNZ
 | | Crystal structure of CreD complex with fumarate | | Descriptor: | CreD, FUMARIC ACID | | Authors: | Katsuyama, Y, Sato, Y, Sugai, Y, Higashiyama, Y, Senda, M, Senda, T, Ohnishi, Y. | | Deposit date: | 2017-05-25 | | Release date: | 2018-03-14 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
FEBS J., 285, 2018
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5H47
 | | Crystal structure of AOL complexed with 2-MeSe-Fuc | | Descriptor: | Uncharacterized protein, methyl 6-deoxy-2-Se-methyl-2-seleno-alpha-L-galactopyranoside | | Authors: | Kato, R, Nishikawa, Y, Makyio, H. | | Deposit date: | 2016-10-31 | | Release date: | 2017-01-25 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Synthesis of seleno-fucose compounds and their application to the X-ray structural determination of carbohydrate-lectin complexes using single/multi-wavelength anomalous dispersion phasing
Bioorg. Med. Chem., 25, 2017
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5GOW
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5XNY
 | | Crystal structure of CreD | | Descriptor: | CreD | | Authors: | Katsuyama, Y, Sato, Y, Sugai, Y, Higashiyama, Y, Senda, M, Senda, T, Ohnishi, Y. | | Deposit date: | 2017-05-25 | | Release date: | 2018-03-14 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination
FEBS J., 285, 2018
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