1WSD
| Alkaline M-protease form I crystal structure | Descriptor: | CALCIUM ION, M-protease, SULFATE ION | Authors: | Shirai, T, Suzuki, A, Yamane, T, Ashida, T, Kobayashi, T, Hitomi, J, Ito, S. | Deposit date: | 2004-11-05 | Release date: | 2004-11-16 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism Protein Eng., 10, 1997
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1Y18
| Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten | Descriptor: | 2-AMINO-5,6-DIMETHYL-BENZIMIDAZOLE-1-PENTANOIC ACID, CHLORIDE ION, Catalytic antibody 34E4 heavy chain, ... | Authors: | Debler, E.W, Ito, S, Heine, A, Wilson, I.A. | Deposit date: | 2004-11-17 | Release date: | 2005-04-05 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural origins of efficient proton abstraction from carbon by a catalytic antibody Proc.Natl.Acad.Sci.USA, 102, 2005
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1Y0L
| Catalytic elimination antibody 34E4 in complex with hapten | Descriptor: | 2-AMINO-5,6-DIMETHYL-BENZIMIDAZOLE-1-PENTANOIC ACID, CHLORIDE ION, Catalytic Antibody Fab 34E4 Heavy chain, ... | Authors: | Debler, E.W, Ito, S, Heine, A, Wilson, I.A. | Deposit date: | 2004-11-15 | Release date: | 2005-04-05 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural origins of efficient proton abstraction from carbon by a catalytic antibody Proc.Natl.Acad.Sci.USA, 102, 2005
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7BXS
| 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycine binding form | Descriptor: | 2-amino-3-ketobutyrate coenzyme A ligase, N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | Deposit date: | 2020-04-20 | Release date: | 2021-04-21 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem, 4, 2021
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7BXQ
| 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator L-Threonine binding form | Descriptor: | 2-amino-3-ketobutyrate coenzyme A ligase, N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | Deposit date: | 2020-04-20 | Release date: | 2021-04-21 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.49 Å) | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem, 4, 2021
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7BXP
| 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator | Descriptor: | 2-amino-3-ketobutyrate coenzyme A ligase | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | Deposit date: | 2020-04-20 | Release date: | 2021-04-21 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem, 4, 2021
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7BXR
| 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline binding form | Descriptor: | (2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid, 2-amino-3-ketobutyrate coenzyme A ligase | Authors: | Motoyama, T, Nakano, S, Hasebe, F, Miyoshi, N, Ito, S. | Deposit date: | 2020-04-20 | Release date: | 2021-04-21 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem, 4, 2021
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6IXF
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6IXE
| Crystal structure of SeMet apo SH3BP5 (I41) | Descriptor: | SH3 domain-binding protein 5, SUCCINIC ACID | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2018-12-10 | Release date: | 2019-03-20 | Last modified: | 2019-03-27 | Method: | X-RAY DIFFRACTION (3.35 Å) | Cite: | Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Life Sci Alliance, 2, 2019
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6IXV
| Crystal structure of SH3BP5-Rab11a | Descriptor: | PHOSPHATE ION, Ras-related protein Rab-11A, SH3 domain-binding protein 5 | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2018-12-12 | Release date: | 2019-03-20 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (3.8 Å) | Cite: | Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Life Sci Alliance, 2, 2019
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6IY9
| Crystal structure of aminoglycoside 7"-phoshotransferase-Ia (APH(7")-Ia/HYG) from Streptomyces hygroscopicus complexed with hygromycin B | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, CITRATE ANION, HYGROMYCIN B VARIANT, ... | Authors: | Takenoya, M, Shimamura, T, Yamanaka, R, Adachi, Y, Ito, S, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2018-12-14 | Release date: | 2019-09-11 | Last modified: | 2019-11-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus. Acta Crystallogr.,Sect.F, 75, 2019
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6J6X
| Crystal structure of apo GGTaseIII | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Geranylgeranyl transferase type-2 subunit beta, MAGNESIUM ION, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-16 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.962 Å) | Cite: | Crystal structure of apo GGTaseIII To Be Published
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6J74
| Complex of GGTaseIII and full-length Ykt6 | Descriptor: | Geranylgeranyl transferase type-2 subunit beta, PHOSPHATE ION, Protein prenyltransferase alpha subunit repeat-containing protein 1, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-16 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.212 Å) | Cite: | Complex of GGTaseIII and full-length Ykt6 To Be Published
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6J7F
| Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP | Descriptor: | DIPHOSPHATE, FARNESYL, GERAN-8-YL GERAN, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-18 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.883 Å) | Cite: | Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP To Be Published
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6IXG
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6J7X
| Complex of GGTaseIII, farnesyl-Ykt6, and GGPP | Descriptor: | FORMIC ACID, GERANYLGERANYL DIPHOSPHATE, Geranylgeranyl transferase type-2 subunit beta, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-18 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP To Be Published
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6KTK
| Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from Paracoccus laeviglucosivorans | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, L-glucono-1,5-lactone, Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity, ... | Authors: | Suzuki, M, Koubara, K, Takenoya, M, Fukano, K, Ito, S, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2019-08-28 | Release date: | 2019-12-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Single amino acid mutation altered substrate specificity for L-glucose and inositol inscyllo-inositol dehydrogenase isolated fromParacoccus laeviglucosivorans. Biosci.Biotechnol.Biochem., 84, 2020
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6KTL
| Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NAD and myo-inositol, from Paracoccus laeviglucosivorans | Descriptor: | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, ACETATE ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | Authors: | Suzuki, M, Koubara, K, Takenoya, M, Fukano, K, Ito, S, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2019-08-28 | Release date: | 2019-12-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Single amino acid mutation altered substrate specificity for L-glucose and inositol inscyllo-inositol dehydrogenase isolated fromParacoccus laeviglucosivorans. Biosci.Biotechnol.Biochem., 84, 2020
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6KTJ
| Crystal structure of scyllo-inositol dehydrogenase R178A mutant, apo-form, from Paracoccus laeviglucosivorans | Descriptor: | ACETATE ION, Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | Authors: | Suzuki, M, Koubara, K, Takenoya, M, Fukano, K, Ito, S, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2019-08-28 | Release date: | 2019-12-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Single amino acid mutation altered substrate specificity for L-glucose and inositol inscyllo-inositol dehydrogenase isolated fromParacoccus laeviglucosivorans. Biosci.Biotechnol.Biochem., 84, 2020
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6LU2
| Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans | Descriptor: | Substrate binding protein | Authors: | Shimamura, K, Akiyama, T, Yokoyama, K, Takenoya, M, Ito, S, Sasaki, Y, Yajima, S. | Deposit date: | 2020-01-25 | Release date: | 2020-03-25 | Last modified: | 2020-04-22 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans. Biochem.Biophys.Res.Commun., 525, 2020
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6LU3
| Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans complexed with 4-hydroxybenzoate hydrazide | Descriptor: | 4-oxidanylbenzohydrazide, Substrate binding protein | Authors: | Shimamura, K, Akiyama, T, Yokoyama, K, Takenoya, M, Ito, S, Sasaki, Y, Yajima, S. | Deposit date: | 2020-01-25 | Release date: | 2020-03-25 | Last modified: | 2020-04-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans. Biochem.Biophys.Res.Commun., 525, 2020
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6LU4
| Crystal structure of the substrate binding protein from Microbacterium hydrocarbonoxydans complexed with propylparaben | Descriptor: | Substrate binding protein, propyl 4-hydroxybenzoate | Authors: | Shimamura, K, Akiyama, T, Yokoyama, K, Takenoya, M, Ito, S, Sasaki, Y, Yajima, S. | Deposit date: | 2020-01-25 | Release date: | 2020-03-25 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans. Biochem.Biophys.Res.Commun., 525, 2020
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7C4N
| Ancestral L-amino acid oxidase (AncLAAO-N5) L-Phe binding form | Descriptor: | Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, PHENYLALANINE | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | Deposit date: | 2020-05-18 | Release date: | 2020-12-02 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids Commun Chem, 3, 2020
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7C4L
| Anncestral L-amino acid oxidase (AncLAAO-N5) L-Gln binding form | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, GLUTAMINE, L-amino acid oxidase | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | Deposit date: | 2020-05-18 | Release date: | 2020-12-02 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids Commun Chem, 3, 2020
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7C4M
| Ancestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form | Descriptor: | Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, TRYPTOPHAN | Authors: | Nakano, S, Minamino, Y, Karasuda, H, Ito, S. | Deposit date: | 2020-05-18 | Release date: | 2020-12-02 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids Commun Chem, 3, 2020
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