6IXG
 
 | |
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
|
|
6IXF
 | |
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
|
|
2YX0
 | | Crystal structure of P. horikoshii TYW1 | | Descriptor: | radical sam enzyme | | Authors: | Goto-Ito, S, Ishii, R, Ito, T, Shibata, R, Fusatomi, E, Sekine, S, Bessho, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-04-23 | | Release date: | 2007-10-30 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.21 Å) | | Cite: | Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis
Acta Crystallogr.,Sect.D, 63, 2007
|
|
1J3Q
 | | Crystal structure of Thermococcus litoralis phosphogrucose isomerase soaked with FeSO4 | | Descriptor: | FE (III) ION, Phosphoglucose Isomerase | | Authors: | Jeong, J.-J, Fushinobu, S, Ito, S, Hidaka, M, Shoun, H, Wakagi, T. | | Deposit date: | 2003-02-11 | | Release date: | 2004-02-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structure of a novel cupin-type phosphoglucose isomerase
To be Published
|
|
6M5W
 | | Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid | | Descriptor: | (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID, GLYCINE, PYRIDOXAL-5'-PHOSPHATE, ... | | Authors: | Ota, T, Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K, Sando, S. | | Deposit date: | 2020-03-11 | | Release date: | 2021-01-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
Iscience, 24, 2021
|
|
6M5O
 | | Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid | | Descriptor: | (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID, GLYCINE, Serine hydroxymethyltransferase, ... | | Authors: | Ota, T, Senoo, A, Ito, S, Ueno, G, Nagatoishi, S, Tsumoto, K, Sando, S. | | Deposit date: | 2020-03-11 | | Release date: | 2021-01-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.30000663 Å) | | Cite: | Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
Iscience, 24, 2021
|
|
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
|
|
5Z76
 | | Artificial L-threonine 3-dehydrogenase designed by full consensus design | | Descriptor: | Artificial L-threonine 3-dehydrogenase | | Authors: | Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S. | | Deposit date: | 2018-01-27 | | Release date: | 2018-08-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
|
|
3VKM
 | | Protease-resistant mutant form of Human Galectin-8 in complex with sialyllactose and lactose | | Descriptor: | 1,2-ETHANEDIOL, Galectin-8, N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose, ... | | Authors: | Yoshida, H, Yamashita, S, Teraoka, M, Nakakita, S, Nishi, N, Kamitori, S. | | Deposit date: | 2011-11-18 | | Release date: | 2012-09-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.98 Å) | | Cite: | X-ray structure of a protease-resistant mutant form of human galectin-8 with two carbohydrate recognition domains
Febs J., 279, 2012
|
|
5Z75
 | | Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction. | | Descriptor: | Artificial L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, NONAETHYLENE GLYCOL, ... | | Authors: | Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S. | | Deposit date: | 2018-01-27 | | Release date: | 2018-08-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
|
|
5Z09
 | | ST0452(Y97N)-UTP binding form | | Descriptor: | Dual sugar-1-phosphate nucleotidylyltransferase, URIDINE 5'-TRIPHOSPHATE | | 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 (2.91 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
|
|
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
|
|
1MPT
 | | CRYSTAL STRUCTURE OF A NEW ALKALINE SERINE PROTEASE (M-PROTEASE) FROM BACILLUS SP. KSM-K16 | | Descriptor: | CALCIUM ION, M-PROTEASE | | Authors: | Yamane, T, Kani, T, Hatanaka, T, Suzuki, A, Ashida, T, Kobayashi, T, Ito, S, Yamashita, O. | | Deposit date: | 1994-04-13 | | Release date: | 1994-06-22 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structure of a new alkaline serine protease (M-protease) from Bacillus sp. KSM-K16.
Acta Crystallogr.,Sect.D, 51, 1995
|
|
1J3P
 | | Crystal structure of Thermococcus litoralis phosphoglucose isomerase | | Descriptor: | FE (III) ION, Phosphoglucose Isomerase | | Authors: | Jeong, J.-J, Fushinobu, S, Ito, S, Hidaka, M, Shoun, H, Wakagi, T. | | Deposit date: | 2003-02-11 | | Release date: | 2004-02-24 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.02 Å) | | Cite: | Crystal structure of a novel cupin-type phosphoglucose isomerase
To be Published
|
|
1J3R
 | | Crystal structure of Thermococcus litoralis phosphogrucose isomerase complexed with gluconate-6-phosphate | | Descriptor: | 6-PHOSPHOGLUCONIC ACID, FE (III) ION, Phosphoglucose Isomerase | | Authors: | Jeong, J.-J, Fushinobu, S, Ito, S, Hidaka, M, Shoun, H, Wakagi, T. | | Deposit date: | 2003-02-11 | | Release date: | 2004-02-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Crystal structure of a novel cupin-type phosphoglucose isomerase
To be Published
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
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
|
|
