7EXU
 
 | | GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside | | Descriptor: | (2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol, Non-reducing end beta-L-arabinofuranosidase, ZINC ION | | Authors: | Maruyama, S, Arakawa, T, Yamada, C, Fujita, K, Fushinobu, S. | | Deposit date: | 2021-05-28 | | Release date: | 2021-11-17 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase.
Glycobiology, 32, 2022
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7DIF
 | | GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution | | Descriptor: | (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol, Non-reducing end beta-L-arabinofuranosidase, POTASSIUM ION, ... | | Authors: | Amaki, S, McGregor, N.G.S, Arakawa, T, Yamada, C, Borlandelli, V, Overkleeft, H.S, Davies, G.J, Fushinobu, S. | | Deposit date: | 2020-11-19 | | Release date: | 2021-01-27 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Angew.Chem.Int.Ed.Engl., 60, 2021
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5WZN
 | | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - GalNAc complex | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, Alpha-N-acetylgalactosaminidase, CALCIUM ION, ... | | Authors: | Sato, M, Arakawa, T, Ashida, H, Fushinobu, S. | | Deposit date: | 2017-01-18 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
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5WZP
 | | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free | | Descriptor: | Alpha-N-acetylgalactosaminidase, CALCIUM ION, ZINC ION | | Authors: | Sato, M, Arakawa, T, Ashida, H, Fushinobu, S. | | Deposit date: | 2017-01-18 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
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5WZQ
 | | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - quadruple mutant | | Descriptor: | Alpha-N-acetylgalactosaminidase, GLYCEROL, ZINC ION | | Authors: | Sato, M, Arakawa, T, Ashida, H, Fushinobu, S. | | Deposit date: | 2017-01-18 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
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5WZR
 | | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex | | Descriptor: | Alpha-N-acetylgalactosaminidase, CALCIUM ION, N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide, ... | | Authors: | Sato, M, Arakawa, T, Ashida, H, Fushinobu, S. | | Deposit date: | 2017-01-18 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.79 Å) | | Cite: | The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
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5YIZ
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5YJ0
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5YJ1
 | | Mouse Cereblon thalidomide binding domain complexed with R-form thalidomide | | Descriptor: | 2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-dione, Protein cereblon, SULFATE ION, ... | | Authors: | Mori, T, Hakoshima, T. | | Deposit date: | 2017-10-06 | | Release date: | 2018-02-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of thalidomide enantiomer binding to cereblon
Sci Rep, 8, 2018
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1H6H
 | | Structure of the PX domain from p40phox bound to phosphatidylinositol 3-phosphate | | Descriptor: | 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE, GLYCEROL, NEUTROPHIL CYTOSOL FACTOR 4 | | Authors: | Karathanassis, D, Bravo, J, Pacold, M, Perisic, O, Williams, R.L. | | Deposit date: | 2001-06-15 | | Release date: | 2001-11-01 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | The Crystal Structure of the Px Domain from P40Phox Bound to Phosphatidylinositol 3-Phosphate
Mol.Cell, 8, 2001
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7EBG
 | | Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7 | | Descriptor: | 3,3-dimethyl-7-(methylamino)-1H-indol-2-one, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Orita, T, Doi, S, Iwanaga, T, Adachi, T. | | Deposit date: | 2021-03-09 | | Release date: | 2021-08-04 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Bioorg.Med.Chem., 44, 2021
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7EAT
 | | Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 1 | | Descriptor: | 1,3-dihydro-2H-indol-2-one, SULFATE ION, [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, ... | | Authors: | Orita, T, Doi, S, Iwanaga, T, Adachi, T. | | Deposit date: | 2021-03-08 | | Release date: | 2021-08-04 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Bioorg.Med.Chem., 44, 2021
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7EBB
 | | Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 2 | | Descriptor: | 1H-pyrrolo[2,3-b]pyridine-3-carbonitrile, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Orita, T, Doi, S, Iwanaga, T, Adachi, T. | | Deposit date: | 2021-03-09 | | Release date: | 2021-08-04 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Bioorg.Med.Chem., 44, 2021
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7EA0
 | | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 1 | | Descriptor: | 1,3-dihydro-2H-indol-2-one, ACETATE ION, CHLORIDE ION, ... | | Authors: | Orita, T, Doi, S, Iwanaga, T, Adachi, T. | | Deposit date: | 2021-03-05 | | Release date: | 2021-08-04 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Bioorg.Med.Chem., 44, 2021
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7EBH
 | | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13 | | Descriptor: | 5-bromanyl-2-methyl-6-propyl-7H-pyrrolo[2,3-d]pyrimidine, ACETATE ION, CHLORIDE ION, ... | | Authors: | Orita, T, Doi, S, Iwanaga, T, Adachi, T. | | Deposit date: | 2021-03-09 | | Release date: | 2021-08-04 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Bioorg.Med.Chem., 44, 2021
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7EAS
 | | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2 | | Descriptor: | 1H-pyrrolo[2,3-b]pyridine-3-carbonitrile, ACETATE ION, CHLORIDE ION, ... | | Authors: | Orita, T, Doi, S, Iwanaga, T, Adachi, T. | | Deposit date: | 2021-03-08 | | Release date: | 2021-08-04 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.97 Å) | | Cite: | Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Bioorg.Med.Chem., 44, 2021
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3WPU
 | | Full-length beta-fructofuranosidase from Microbacterium saccharophilum K-1 | | Descriptor: | Beta-fructofuranosidase, GLYCEROL | | Authors: | Yokoi, G, Mori, M, Sato, S, Miyazaki, T, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2014-01-17 | | Release date: | 2014-03-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 beta-fructofuranosidase
Appl.Microbiol.Biotechnol., 98, 2014
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3WPV
 | | Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/F447V/F470Y/P500S | | Descriptor: | Beta-fructofuranosidase, GLYCEROL | | Authors: | Yokoi, G, Mori, M, Sato, S, Miyazaki, T, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2014-01-17 | | Release date: | 2014-03-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 beta-fructofuranosidase
Appl.Microbiol.Biotechnol., 98, 2014
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3WPY
 | | Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/S200T/F447V/P500S | | Descriptor: | Beta-fructofuranosidase | | Authors: | Yokoi, G, Mori, M, Sato, S, Miyazaki, T, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2014-01-17 | | Release date: | 2014-03-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 beta-fructofuranosidase
Appl.Microbiol.Biotechnol., 98, 2014
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3WPZ
 | | Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/S200T/F447P/F470Y/P500S | | Descriptor: | Beta-fructofuranosidase | | Authors: | Yokoi, G, Mori, M, Sato, S, Miyazaki, T, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2014-01-17 | | Release date: | 2014-03-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.27 Å) | | Cite: | Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 beta-fructofuranosidase
Appl.Microbiol.Biotechnol., 98, 2014
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3B13
 | | Crystal structure of the DHR-2 domain of DOCK2 in complex with Rac1 (T17N mutant) | | Descriptor: | Dedicator of cytokinesis protein 2, Ras-related C3 botulinum toxin substrate 1 | | Authors: | Hanawa-Suetsugu, K, Kukimoto-Niino, M, Mishima-Tsumagari, C, Terada, T, Shirouzu, M, Fukui, Y, Yokoyama, S. | | Deposit date: | 2011-06-24 | | Release date: | 2012-03-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.006 Å) | | Cite: | Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proc.Natl.Acad.Sci.USA, 109, 2012
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4YOU
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4YOR
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4YOT
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3A4T
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