5Z0A
| ST0452(Y97N)-GlcNAc binding form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Dual sugar-1-phosphate nucleotidylyltransferase | Authors: | Honda, Y, Nakano, S, Ito, S, Dadashipour, M, Zhang, Z, Kawarabayasi, Y. | Deposit date: | 2017-12-19 | Release date: | 2018-10-31 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Improvement of ST0452N-Acetylglucosamine-1-Phosphate Uridyltransferase Activity by the Cooperative Effect of Two Single Mutations Identified through Structure-Based Protein Engineering Appl. Environ. Microbiol., 84, 2018
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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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2D22
| Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | Descriptor: | ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, SULFATE ION, ... | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | Deposit date: | 2005-09-02 | Release date: | 2006-10-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86 J.Biochem., 146, 2009
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2D1Z
| Crystal structure of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | Descriptor: | ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, SULFATE ION | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | Deposit date: | 2005-09-02 | Release date: | 2006-10-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86 J.Biochem., 146, 2009
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2D20
| Crystal structure of michaelis complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | Descriptor: | ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, P-NITROPHENOL, ... | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | Deposit date: | 2005-09-02 | Release date: | 2006-10-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86 J.Biochem., 146, 2009
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2D23
| Crystal structure of EP complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | Descriptor: | AZIDE ION, ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, ... | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | Deposit date: | 2005-09-02 | Release date: | 2006-10-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86 J.Biochem., 146, 2009
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2ZZN
| The complex structure of aTrm5 and tRNACys | Descriptor: | MAGNESIUM ION, RNA (71-MER), S-ADENOSYLMETHIONINE, ... | Authors: | Goto-Ito, S, Ito, T, Yokoyama, S. | Deposit date: | 2009-02-19 | Release date: | 2009-09-15 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat.Struct.Mol.Biol., 16, 2009
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7X7I
| Ancestral L-Lys oxidase (AncLLysO-2) ligand free form | Descriptor: | FAD dependent enzyme, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Motoyama, T, Ishida, C, Hasebe, F, Ito, S, Nakano, S. | Deposit date: | 2022-03-09 | Release date: | 2023-01-18 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Acs Omega, 7, 2022
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7X7K
| Ancestral L-Lys oxidase (AncLLysO-2) L-Arg binding form | Descriptor: | ARGININE, FAD dependent enzyme, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Motoyama, T, Ishida, C, Hasebe, F, Ito, S, Nakano, S. | Deposit date: | 2022-03-09 | Release date: | 2023-01-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Acs Omega, 7, 2022
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7X7J
| Ancestral L-Lys oxidase (AncLLysO-2) L-Lys binding form | Descriptor: | FAD dependent enzyme, FLAVIN-ADENINE DINUCLEOTIDE, LYSINE | Authors: | Motoyama, T, Ishida, C, Hasebe, F, Ito, S, Nakano, S. | Deposit date: | 2022-03-09 | Release date: | 2023-01-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Acs Omega, 7, 2022
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2ZZM
| The complex structure of aTrm5 and tRNALeu | Descriptor: | MAGNESIUM ION, RNA (84-MER), S-ADENOSYLMETHIONINE, ... | Authors: | Goto-Ito, S, Ito, T, Yokoyama, S. | Deposit date: | 2009-02-19 | Release date: | 2009-09-15 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation Nat.Struct.Mol.Biol., 16, 2009
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2D24
| Crystal structure of ES complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86 | Descriptor: | ENDO-1,4-BETA-D-XYLANASE, GLYCEROL, SULFATE ION, ... | Authors: | Suzuki, R, Kuno, A, Fujimoto, Z, Ito, S, Kawahara, S.I, Kaneko, S, Hasegawa, T, Taira, K. | Deposit date: | 2005-09-02 | Release date: | 2006-10-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86 J.Biochem., 146, 2009
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3AXZ
| Crystal structure of Haemophilus influenzae TrmD in complex with adenosine | Descriptor: | ADENOSINE, tRNA (guanine-N(1)-)-methyltransferase | Authors: | Yoshida, K, Goto-Ito, S, Ito, T, Hou, Y.M, Yokoyama, S. | Deposit date: | 2011-04-21 | Release date: | 2011-08-17 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. Rna, 17, 2011
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3AY0
| Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine | Descriptor: | ADENOSINE, Uncharacterized protein MJ0883, ZINC ION | Authors: | Goto-Ito, S, Ito, T, Hou, Y.M, Yokoyama, S. | Deposit date: | 2011-04-21 | Release date: | 2011-08-17 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.05 Å) | Cite: | Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. Rna, 17, 2011
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2YX1
| Crystal structure of M.jannaschii tRNA m1G37 methyltransferase | Descriptor: | Hypothetical protein MJ0883, SINEFUNGIN, ZINC ION | Authors: | Goto-Ito, S, Ito, T, Ishii, R, Bessho, Y, Yokoyama, S. | Deposit date: | 2007-04-23 | Release date: | 2008-04-22 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins, 72, 2008
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7C86
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2020-05-28 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E6Z
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 microsecond structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E6X
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E71
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E70
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E6Y
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7CMF
| Crystal structure of human P-cadherin REC12 (monomer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor) | Descriptor: | 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine, CALCIUM ION, Cadherin-3 | Authors: | Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K. | Deposit date: | 2020-07-27 | Release date: | 2021-09-15 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion Commun Biol, 4, 2021
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