5GHP
| Crystal structure of human MTH1(G2K/D120A mutant) in complex with 2-oxo-dATP | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION | Authors: | Nakamura, T, Waz, S, Hirata, K, Nakabeppu, Y, Yamagata, Y. | Deposit date: | 2016-06-20 | Release date: | 2017-01-04 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.192 Å) | Cite: | Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity J. Biol. Chem., 292, 2017
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5B36
| Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with Cysteine | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CYSTEINE, PYRIDOXAL-5'-PHOSPHATE, ... | Authors: | Nakamura, T, Takeda, E, Kawai, Y, Kataoka, M, Ishikawa, K. | Deposit date: | 2016-02-10 | Release date: | 2016-03-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1 Extremophiles, 20, 2016
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5B3A
| Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid, Protein CysO | Authors: | Nakamura, T, Takeda, E, Kawai, Y, Kataoka, M, Ishikawa, K. | Deposit date: | 2016-02-12 | Release date: | 2016-03-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.14 Å) | Cite: | Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1 Extremophiles, 20, 2016
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6ILI
| Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 6.5 | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE | Authors: | Nakamura, T, Waz, S, Hirata, K, Nakabeppu, Y, Yamagata, Y. | Deposit date: | 2018-10-18 | Release date: | 2018-11-07 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity J. Biol. Chem., 292, 2017
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6LCS
| Crystal structure of 73MuL9 Fv-clasp fragment in complex with GA-pyridine analogue | Descriptor: | (2~{S})-6-[4-(hydroxymethyl)-3-oxidanyl-pyridin-1-ium-1-yl]-2-(phenylmethoxycarbonylamino)hexanoic acid, PHOSPHATE ION, VH-SARAH, ... | Authors: | Nakamura, T, Takagi, J, Yamagata, Y, Morioka, H. | Deposit date: | 2019-11-19 | Release date: | 2020-11-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Molecular recognition of a single-chain Fv antibody specific for GA-pyridine, an advanced glycation end-product (AGE), elucidated using biophysical techniques and synthetic antigen analogues. J.Biochem., 170, 2021
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6ITZ
| Peroxiredoxin from Thermococcus kodakaraensis | Descriptor: | Peroxiredoxin | Authors: | Nakamura, T, Himiyama, T. | Deposit date: | 2018-11-27 | Release date: | 2019-03-06 | Last modified: | 2019-07-17 | Method: | X-RAY DIFFRACTION (2.96 Å) | Cite: | Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis. J.Biochem., 166, 2019
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6IU1
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6IU0
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2CZN
| Solution structure of the chitin-binding domain of hyperthermophilic chitinase from pyrococcus furiosus | Descriptor: | chitinase | Authors: | Uegaki, T, Ikegami, T, Nakamura, T, Hagihara, Y, Mine, S, Inoue, T, Matsumura, H, Ataka, M, Ishikawa, K. | Deposit date: | 2005-07-13 | Release date: | 2006-07-18 | Last modified: | 2022-03-09 | Method: | SOLUTION NMR | Cite: | Tertiary structure and carbohydrate recognition by the chitin-binding domain of a hyperthermophilic chitinase from Pyrococcus furiosus. J.Mol.Biol., 381, 2008
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3WL3
| N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii | Descriptor: | GLYCEROL, PHOSPHATE ION, Putative uncharacterized protein PH0499, ... | Authors: | Nakamura, T, Niiyama, M, Hashimoto, W, Uegaki, K. | Deposit date: | 2013-11-07 | Release date: | 2014-05-07 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase Febs J., 281, 2014
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3WL4
| N,N'-diacetylchitobiose deacetylase (Se-derivative) from Pyrococcus furiosus | Descriptor: | CADMIUM ION, CALCIUM ION, CHLORIDE ION, ... | Authors: | Nakamura, T, Niiyama, M, Hashimoto, W, Uegaki, K. | Deposit date: | 2013-11-07 | Release date: | 2014-05-07 | Last modified: | 2014-08-20 | Method: | X-RAY DIFFRACTION (1.54 Å) | Cite: | Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase Febs J., 281, 2014
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2CWR
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5LAM
| Refined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli | Descriptor: | Inner membrane protein YgaP | Authors: | Eichmann, C, Tzitzilonis, C, Nakamura, T, Maslennikov, I, Kwiatkowski, W, Choe, S, Lipton, S.A, Guntert, P, Riek, R. | Deposit date: | 2016-06-14 | Release date: | 2016-08-17 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein. J.Mol.Biol., 428, 2016
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5LAO
| S-nitrosylated 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli | Descriptor: | Inner membrane protein YgaP | Authors: | Eichmann, C, Tzitzilonis, C, Nakamura, T, Maslennikov, I, Kwiatkowski, W, Choe, S, Lipton, S.A, Guntert, P, Riek, R. | Deposit date: | 2016-06-14 | Release date: | 2016-08-17 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein. J.Mol.Biol., 428, 2016
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3NG5
| Crystal Structure of V30M transthyretin complexed with (-)-epigallocatechin gallate (EGCG) | Descriptor: | (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate, GLYCEROL, Transthyretin | Authors: | Miyata, M, Nakamura, T, Ikemizu, S, Chirifu, M, Yamagata, Y, Kai, H. | Deposit date: | 2010-06-11 | Release date: | 2010-07-07 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structure of green tea polyphenol(-)-epigallocatechin gallate (EGCG)-transthyretin complex reveals novel binding site distinct from thyroxine binding site Biochemistry, 2010
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8HH0
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8HLA
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5XDH
| His/DOPA ligated cytochrome c from an anammox organism KSU-1 | Descriptor: | ACETATE ION, HEME C, Putative cytochrome c, ... | Authors: | Hira, D, Kitamura, R, Nakamura, T, Yamagata, Y, Furukawa, K, Fujii, T. | Deposit date: | 2017-03-28 | Release date: | 2018-03-28 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (1.32 Å) | Cite: | Anammox Organism KSU-1 Expresses a Novel His/DOPA Ligated Cytochrome c. J. Mol. Biol., 430, 2018
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7X1L
| Malate dehydrogenase from Geobacillus stearothermophilus (gs-MDH) delta E311 mutant complexed with Nicotinamide Adenine Dinucleotide (NAD+) | Descriptor: | Malate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Shimozawa, Y, Himiyama, T, Nakamura, T, Nishiya, Y. | Deposit date: | 2022-02-24 | Release date: | 2022-10-19 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.28 Å) | Cite: | Reducing substrate inhibition of malate dehydrogenase from Geobacillus stearothermophilus by C-terminal truncation. Protein Eng.Des.Sel., 35, 2022
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2ZHK
| Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer (crystal 1) | Descriptor: | Galectin-9, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Nagae, M, Nishi, N, Murata, T, Usui, T, Nakamura, T, Wakatsuki, S, Kato, R. | Deposit date: | 2008-02-06 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology, 19, 2009
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2ZHL
| Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer (crystal 2) | Descriptor: | Galectin-9, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Nagae, M, Nishi, N, Murata, T, Usui, T, Nakamura, T, Wakatsuki, S, Kato, R. | Deposit date: | 2008-02-06 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology, 19, 2009
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2ZHN
| Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine trimer (crystal 2) | Descriptor: | (R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL, GALECTIN-9, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Nagae, M, Nishi, N, Murata, T, Usui, T, Nakamura, T, Wakatsuki, S, Kato, R. | Deposit date: | 2008-02-06 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology, 19, 2009
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2ZHM
| Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine trimer (crystal 1) | Descriptor: | (R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL, Galectin-9, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nagae, M, Nishi, N, Murata, T, Usui, T, Nakamura, T, Wakatsuki, S, Kato, R. | Deposit date: | 2008-02-06 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology, 19, 2009
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5HBP
| The crystal of rhodanese domain of YgaP treated with SNOC | Descriptor: | Inner membrane protein YgaP | Authors: | Eichmann, C, Tzitzilonis, C, Nakamura, T, Kwiatkowski, W, Maslennikov, I, Choe, S, Lipton, S.A, Riek, R. | Deposit date: | 2016-01-01 | Release date: | 2016-08-10 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein. J.Mol.Biol., 428, 2016
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5HBL
| Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated | Descriptor: | Inner membrane protein YgaP | Authors: | Eichmann, C, Tzitzilonis, C, Nakamura, T, Kwiatkowski, W, Maslennikov, I, Choe, S, Lipton, S.A, Riek, R. | Deposit date: | 2015-12-31 | Release date: | 2016-08-10 | Last modified: | 2021-09-08 | Method: | X-RAY DIFFRACTION (1.617 Å) | Cite: | S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein. J.Mol.Biol., 428, 2016
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