5X4Q
 
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 7 | | Descriptor: | 1,2-ETHANEDIOL, 5-[[5-chloranyl-2-(pyridin-3-ylmethylamino)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one, B-cell lymphoma 6 protein, ... | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-02-13 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach
J. Med. Chem., 60, 2017
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5X4N
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 4 | | Descriptor: | 1,2-ETHANEDIOL, 5-chloro-N4-phenylpyrimidine-2,4-diamine, B-cell lymphoma 6 protein | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-02-13 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach
J. Med. Chem., 60, 2017
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5X4O
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 5 | | Descriptor: | B-cell lymphoma 6 protein, N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-02-13 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach
J. Med. Chem., 60, 2017
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5X4M
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 1 | | Descriptor: | B-cell lymphoma 6 protein, N-phenyl-1,3,5-triazine-2,4-diamine | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-02-13 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach
J. Med. Chem., 60, 2017
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5X4P
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 6 | | Descriptor: | 5-[(5-chloranylpyrimidin-4-yl)amino]-1,3-dihydroindol-2-one, B-cell lymphoma 6 protein | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-02-13 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach
J. Med. Chem., 60, 2017
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5X9O
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 1a | | Descriptor: | 1,2-ETHANEDIOL, 5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one, B-cell lymphoma 6 protein, ... | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-03-08 | | Release date: | 2017-08-16 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design
Bioorg. Med. Chem., 25, 2017
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5X9P
 | | Crystal structure of the BCL6 BTB domain in complex with Compound 5 | | Descriptor: | 3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid, B-cell lymphoma 6 protein | | Authors: | Sogabe, S, Ida, K, Lane, W, Snell, G. | | Deposit date: | 2017-03-08 | | Release date: | 2017-08-16 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design
Bioorg. Med. Chem., 25, 2017
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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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5B2E
 | | N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii complexed with its inhibitor MPG (acetate-containing condition) | | Descriptor: | 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose, HEXANE-1,6-DIOL, Putative uncharacterized protein PH0499, ... | | Authors: | Nakamura, T, Niiyama, M, Ida, K, Uegaki, K. | | Deposit date: | 2016-01-15 | | Release date: | 2016-08-10 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii
J.Struct.Biol., 195, 2016
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5B2F
 | | N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii complexed with its inhibitor MPG (phosphate-containing condition) | | Descriptor: | 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose, Putative uncharacterized protein PH0499, ZINC ION | | Authors: | Nakamura, T, Niiyama, M, Ida, K, Uegaki, K. | | Deposit date: | 2016-01-15 | | Release date: | 2016-08-10 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii
J.Struct.Biol., 195, 2016
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1ULQ
 | | Crystal structure of tt0182 from Thermus thermophilus HB8 | | Descriptor: | putative acetyl-CoA acetyltransferase | | Authors: | Ago, H, Hamada, K, Ida, K, Kanda, H, Sugahara, M, Yamamoto, M, Kuroishi, C, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-16 | | Release date: | 2004-11-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of tt0182 from Thermus thermophilus HB8
To be Published
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1V25
 | | Crystal structure of tt0168 from Thermus thermophilus HB8 | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, long-chain-fatty-acid-CoA synthetase | | Authors: | Hisanaga, Y, Ago, H, Nakatsu, T, Hamada, K, Ida, K, Kanda, H, Yamamoto, M, Hori, T, Arii, Y, Sugahara, M, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-07 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural Basis of the Substrate-specific Two-step Catalysis of Long Chain Fatty Acyl-CoA Synthetase Dimer
J.Biol.Chem., 279, 2004
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1V8E
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1ULT
 | | Crystal structure of tt0168 from Thermus thermophilus HB8 | | Descriptor: | CITRIC ACID, long chain fatty acid-CoA ligase | | Authors: | Hisanaga, Y, Ago, H, Nakatsu, T, Hamada, K, Ida, K, Kanda, H, Yamamoto, M, Hori, T, Arii, Y, Sugahara, M, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-16 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural basis of the substrate specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer
J.Biol.Chem., 279, 2004
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1V26
 | | Crystal structure of tt0168 from Thermus thermophilus HB8 | | Descriptor: | ADENOSINE MONOPHOSPHATE, MAGNESIUM ION, MYRISTIC ACID, ... | | Authors: | Hisanaga, Y, Ago, H, Nakatsu, T, Hamada, K, Ida, K, Kanda, H, Yamamoto, M, Hori, T, Arii, Y, Sugahara, M, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-07 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural Basis of the Substrate-specific Two-step Catalysis of Long Chain Fatty Acyl-CoA Synthetase Dimer
J.Biol.Chem., 279, 2004
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1ULU
 | | Crystal structure of tt0143 from Thermus thermophilus HB8 | | Descriptor: | enoyl-acyl carrier protein reductase | | Authors: | Ago, H, Hamada, K, Ida, K, Kanda, H, Sugahara, M, Yamamoto, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-16 | | Release date: | 2004-11-02 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of tt0143 from Thermus thermophilus HB8
To be Published
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2ZHJ
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2ZHI
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3AD8
 | | Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate | | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Suzuki, H, Moriguchi, T, Ida, K. | | Deposit date: | 2010-01-15 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.
J.Biochem., 148, 2010
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3ADA
 | | Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with sulfite | | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Suzuki, H, Moriguchi, T, Ida, K. | | Deposit date: | 2010-01-15 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.
J.Biochem., 148, 2010
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3AD7
 | | Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate | | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Suzuki, H, Moriguchi, T, Ida, K. | | Deposit date: | 2010-01-15 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.
J.Biochem., 148, 2010
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3AD9
 | | Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 sarcosine-reduced form | | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Suzuki, H, Moriguchi, T, Ida, K. | | Deposit date: | 2010-01-15 | | Release date: | 2010-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.
J.Biochem., 148, 2010
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7PCO
 | | BurG E232Q mutant (holo) in complex with 2R,3R-2,3-dihydroxy-6-methyl-heptanoate (12): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (2R,3R)-6-methyl-2,3-bis(oxidanyl)heptanoic acid, GLYCEROL, Ketol-acid reductoisomerase, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCT
 | | BurG E232Q mutant (holo) in complex with enol-oxalacetate (15): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (~{Z})-2-oxidanylbut-2-enedioic acid, GLYCEROL, Ketol-acid reductoisomerase, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-04 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCC
 | | BurG in complex with Mg2+ and NAD+ (holo): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | GLYCEROL, Ketol-acid reductoisomerase, MAGNESIUM ION, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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