5AXC
 
 | | Crystal structure of mouse SAHH complexed with 3'-keto aristeromycin | | Descriptor: | (2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-2-hydroxy-5-(hydroxymethyl)cyclopentanone, Adenosylhomocysteinase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Kusakabe, Y, Ishihara, M, Tanaka, N. | | Deposit date: | 2015-07-24 | | Release date: | 2016-07-27 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal structure of mouse SAHH complexed with 3'-keto aristeromycin
To Be Published
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5AXD
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5AXB
 | | Crystal structure of mouse SAHH complexed with noraristeromycin | | Descriptor: | (1S,2R,3S,4R)-4-(6-aminopurin-9-yl)cyclopentane-1,2,3-triol, Adenosylhomocysteinase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Kusakabe, Y, Ishihara, M, Tanaka, N. | | Deposit date: | 2015-07-24 | | Release date: | 2016-07-27 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structure of mouse SAHH complexed with noraristeromycin
To Be Published
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5AXA
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4X8Y
 | | Crystal structure of human PGRMC1 cytochrome b5-like domain | | Descriptor: | Membrane-associated progesterone receptor component 1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nakane, T, Yamamoto, T, Shimamura, T, Kobayashi, T, Kabe, Y, Suematsu, M. | | Deposit date: | 2014-12-11 | | Release date: | 2016-03-23 | | Last modified: | 2020-02-05 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance
Nat Commun, 7, 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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6IMF
 | | Crystal structure of TOXIN/ANTITOXIN complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Cysteine-rich venom protein triflin, GLYCEROL, ... | | Authors: | Shioi, N, Tadokoro, T, Shioi, S, Hu, Y, Kurahara, L.H, Okabe, Y, Matsubara, H, Kita, S, Ose, T, Kuroki, K, Maenaka, K, Terada, S. | | Deposit date: | 2018-10-22 | | Release date: | 2018-12-12 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake.
J. Biol. Chem., 294, 2019
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4WCO
 | | Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A | | Descriptor: | ACETATE ION, C-type lectin domain family 2 member D, SULFATE ION, ... | | Authors: | Kita, S, Matsubara, H, Kasai, Y, Tamaoki, T, Okabe, Y, Fukuhara, H, Kamishikiryo, J, Ose, T, Kuroki, K, Maenaka, K. | | Deposit date: | 2014-09-05 | | Release date: | 2015-06-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.46 Å) | | Cite: | Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A
Eur.J.Immunol., 45, 2015
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5WS7
 | | Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 2-oxo-dATP | | 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, Waz, S, Hirata, K, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2016-12-05 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1 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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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
 | | 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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5GHN
 | | Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP | | 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, 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 (1.391 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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5GHM
 | | Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 7.0 | | 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 (1.5 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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5JR8
 | | Disposal of Iron by a Mutant form of Siderocalin NGAL | | Descriptor: | GLYCEROL, Neutrophil gelatinase-associated lipocalin, PHOSPHATE ION | | Authors: | Rupert, P.B, Strong, R.K, Barasch, J, Hollman, M, Deng, R, Hod, E.A, Abergel, R, Allred, B, Xu, K, Darrah, S, Tekabe, Y, Perlstein, A, Bruck, E, Stauber, J, Corbin, K, Buchen, C, Slavkovich, V, Graziano, J, Spitalnik, S, Qiu, A. | | Deposit date: | 2016-05-05 | | Release date: | 2016-09-28 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Disposal of iron by a mutant form of lipocalin 2.
Nat Commun, 7, 2016
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5GHQ
 | | Crystal structure of human MTH1(G2K/D120A mutant) in complex with 2-oxo-dATP under high concentrations of 2-oxo-dATP | | 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, 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 (1.181 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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5GHJ
 | | Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP | | 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, 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 (1.2 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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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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7EF9
 | | Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form II) | | Descriptor: | Adenine DNA glycosylase, DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3'), ... | | Authors: | Nakamura, T, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2021-03-21 | | Release date: | 2021-06-23 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.97 Å) | | Cite: | Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Nucleic Acids Res., 49, 2021
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7EF8
 | | Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form I) | | Descriptor: | Adenine DNA glycosylase, DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3'), DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3'), ... | | Authors: | Nakamura, T, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2021-03-21 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Nucleic Acids Res., 49, 2021
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7EFA
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1WDY
 | | Crystal structure of ribonuclease | | Descriptor: | 2-5A-dependent ribonuclease, 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE | | Authors: | Tanaka, N, Nakanishi, M, Kusakabe, Y, Goto, Y, Kitade, Y, Nakamura, K.T. | | Deposit date: | 2004-05-19 | | Release date: | 2004-10-05 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L
Embo J., 23, 2004
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1V8B
 | | Crystal structure of a hydrolase | | Descriptor: | ADENOSINE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, adenosylhomocysteinase | | Authors: | Tanaka, N, Nakanishi, M, Kusakabe, Y, Shiraiwa, K, Kitade, Y, Nakamura, K.T. | | Deposit date: | 2004-01-03 | | Release date: | 2004-10-26 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal Structure of S-Adenosyl-l-Homocysteine Hydrolase from the Human Malaria Parasite Plasmodium falciparum
J.Mol.Biol., 343, 2004
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2DLC
 | | Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase | | Descriptor: | MAGNESIUM ION, O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE, T-RNA (76-MER), ... | | Authors: | Tsunoda, M, Kusakabe, Y, Tanaka, N, Nakamura, K.T. | | Deposit date: | 2006-04-18 | | Release date: | 2007-06-12 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.
Nucleic Acids Res., 35, 2007
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1IRY
 | | Solution structure of the hMTH1, a nucleotide pool sanitization enzyme | | Descriptor: | hMTH1 | | Authors: | Mishima, M, Itoh, N, Sakai, Y, Kamiya, H, Nakabeppu, Y, Shirakawa, M. | | Deposit date: | 2001-10-25 | | Release date: | 2003-12-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates
J.Biol.Chem., 279, 2004
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3WH2
 | | Human Mincle in complex with citrate | | Descriptor: | C-type lectin domain family 4 member E, CALCIUM ION, CITRATE ANION | | Authors: | Furukawa, A, Kamishikiryo, J, Mori, D, Toyonaga, K, Okabe, Y, Toji, A, Kanda, R, Miyake, Y, Ose, T, Yamasaki, S, Maenaka, K. | | Deposit date: | 2013-08-21 | | Release date: | 2013-10-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL
Proc.Natl.Acad.Sci.USA, 110, 2013
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