8XY0
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![BU of 8xy0 by Molmil](/molmil-images/mine/8xy0) | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, Endo-1,4-beta-xylanase A | Authors: | Nakamura, T, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | Deposit date: | 2024-01-19 | Release date: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR. Sci Rep, 14, 2024
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8Y1M
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![BU of 8y1m by Molmil](/molmil-images/mine/8y1m) | Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose. | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ... | Authors: | Nakamura, T, Kuwata, K, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | Deposit date: | 2024-01-25 | Release date: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR. Sci Rep, 14, 2024
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6LCS
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![BU of 6lcs by Molmil](/molmil-images/mine/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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2NVL
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![BU of 2nvl by Molmil](/molmil-images/mine/2nvl) | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form) | Descriptor: | Probable peroxiredoxin | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | Deposit date: | 2006-11-13 | Release date: | 2007-11-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.36 Å) | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate Proc.Natl.Acad.Sci.Usa, 105, 2008
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8I1C
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![BU of 8i1c by Molmil](/molmil-images/mine/8i1c) | |
8I1A
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![BU of 8i1a by Molmil](/molmil-images/mine/8i1a) | |
8I1I
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![BU of 8i1i by Molmil](/molmil-images/mine/8i1i) | Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 7.7 | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Nakamura, T, Yamagata, Y. | Deposit date: | 2023-01-13 | Release date: | 2023-03-22 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Febs Lett., 597, 2023
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8I1D
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![BU of 8i1d by Molmil](/molmil-images/mine/8i1d) | Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP at pH 7.7 | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Nakamura, T, Yamagata, Y. | Deposit date: | 2023-01-13 | Release date: | 2023-03-22 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Febs Lett., 597, 2023
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8I1E
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![BU of 8i1e by Molmil](/molmil-images/mine/8i1e) | Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP at pH 8.0 | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Nakamura, T, Yamagata, Y. | Deposit date: | 2023-01-13 | Release date: | 2023-03-22 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Febs Lett., 597, 2023
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8I19
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![BU of 8i19 by Molmil](/molmil-images/mine/8i19) | |
8I18
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![BU of 8i18 by Molmil](/molmil-images/mine/8i18) | |
8I1H
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![BU of 8i1h by Molmil](/molmil-images/mine/8i1h) | |
8I1J
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![BU of 8i1j by Molmil](/molmil-images/mine/8i1j) | Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 9.7 | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Nakamura, T, Yamagata, Y. | Deposit date: | 2023-01-13 | Release date: | 2023-03-22 | Last modified: | 2023-07-26 | Method: | X-RAY DIFFRACTION (1.08 Å) | Cite: | Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Febs Lett., 597, 2023
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8I8T
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8I1F
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![BU of 8i1f by Molmil](/molmil-images/mine/8i1f) | Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP at pH 8.6 | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Nakamura, T, Yamagata, Y. | Deposit date: | 2023-01-13 | Release date: | 2023-03-22 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.05 Å) | Cite: | Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Febs Lett., 597, 2023
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8I8S
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8I1G
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6LFW
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![BU of 6lfw by Molmil](/molmil-images/mine/6lfw) | |
3VOV
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![BU of 3vov by Molmil](/molmil-images/mine/3vov) | Crystal Structure of ROK Hexokinase from Thermus thermophilus | Descriptor: | GLYCEROL, Glucokinase, ZINC ION | Authors: | Nakamura, T, Kashima, Y, Mine, S, Oku, T, Uegaki, K. | Deposit date: | 2012-02-21 | Release date: | 2012-06-27 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.02 Å) | Cite: | Characterization and crystal structure of the thermophilic ROK hexokinase from Thermus thermophilus J.Biosci.Bioeng., 2012
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6LFV
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8WWY
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![BU of 8wwy by Molmil](/molmil-images/mine/8wwy) | Crystal structure of mouse TIFA/TIFAB heterodimer | Descriptor: | (2R,5R)-hexane-2,5-diol, TRAF-interacting protein with FHA domain-containing protein A, TRAF-interacting protein with FHA domain-containing protein B | Authors: | Nakamura, T. | Deposit date: | 2023-10-27 | Release date: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.79 Å) | Cite: | TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA. Proc.Natl.Acad.Sci.USA, 121, 2024
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3VSD
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![BU of 3vsd by Molmil](/molmil-images/mine/3vsd) | Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, O-ACETYLSERINE, PYRIDOXAL-5'-PHOSPHATE, ... | Authors: | Nakamura, T, Kawai, Y, Kataoka, M, Ishikawa, K. | Deposit date: | 2012-04-24 | Release date: | 2012-05-16 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1 J.Mol.Biol., 422, 2012
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3VSC
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![BU of 3vsc by Molmil](/molmil-images/mine/3vsc) | Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Phospho-L-Serine | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, PHOSPHOSERINE, PYRIDOXAL-5'-PHOSPHATE, ... | Authors: | Nakamura, T, Kawai, Y, Kataoka, M, Ishikawa, K. | Deposit date: | 2012-04-24 | Release date: | 2012-05-16 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.07 Å) | Cite: | Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1 J.Mol.Biol., 422, 2012
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5GHI
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![BU of 5ghi by Molmil](/molmil-images/mine/5ghi) | Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 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 (1.211 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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5GHO
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![BU of 5gho by Molmil](/molmil-images/mine/5gho) | Crystal structure of human MTH1(G2K/D120A mutant) in complex with 8-oxo-dGTP | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, GLYCEROL, ... | 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 (1.191 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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