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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7B81
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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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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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7F4Z
 | | X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with ADP | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, CHLORIDE ION, Heat shock 70 kDa protein 1B, ... | | Authors: | Yokoyama, T, Fujii, S, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2021-06-21 | | Release date: | 2022-06-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP.
Iucrj, 9, 2022
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7F50
 | | X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with AMPPnP | | Descriptor: | CHLORIDE ION, Heat shock 70 kDa protein 1B, MAGNESIUM ION, ... | | Authors: | Yokoyama, T, Fujii, S, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2021-06-21 | | Release date: | 2022-06-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.703 Å) | | Cite: | Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP.
Iucrj, 9, 2022
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2ZX0
 | | Rhamnose-binding lectin CSL3 | | Descriptor: | CSL3, GLYCEROL, PHOSPHATE ION | | Authors: | Shirai, T, Watababe, Y, Lee, M, Ogawa, T, Muramoto, K. | | Deposit date: | 2008-12-19 | | Release date: | 2009-06-30 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein
J.Mol.Biol., 391, 2009
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2ZX2
 | | Rhamnose-binding lectin CSL3 | | Descriptor: | CSL3, PHOSPHATE ION, alpha-L-rhamnopyranose | | Authors: | Shirai, T, Watababe, Y, Lee, M, Ogawa, T, Muramoto, K. | | Deposit date: | 2008-12-19 | | Release date: | 2009-06-30 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein
J.Mol.Biol., 391, 2009
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2ZX1
 | | Rhamnose-binding lectin CSL3 | | Descriptor: | CSL3, PHOSPHATE ION | | Authors: | Shirai, T, Watababe, Y, Lee, M, Ogawa, T, Muramoto, K. | | Deposit date: | 2008-12-19 | | Release date: | 2009-06-30 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein
J.Mol.Biol., 391, 2009
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2ZX4
 | | Rhamnose-binding lectin CSL3 | | Descriptor: | CSL3, PHOSPHATE ION, alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose, ... | | Authors: | Shirai, T, Watababe, Y, Lee, M, Ogawa, T, Muramoto, K. | | Deposit date: | 2008-12-19 | | Release date: | 2009-06-30 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein
J.Mol.Biol., 391, 2009
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2ZX3
 | | Rhamnose-binding lectin CSL3 | | Descriptor: | CSL3, PHOSPHATE ION, alpha-D-galactopyranose-(1-6)-beta-D-glucopyranose | | Authors: | Shirai, T, Watababe, Y, Lee, M, Ogawa, T, Muramoto, K. | | Deposit date: | 2008-12-19 | | Release date: | 2009-06-30 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein
J.Mol.Biol., 391, 2009
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1J1I
 | | Crystal structure of a His-tagged Serine Hydrolase Involved in the Carbazole Degradation (CarC enzyme) | | Descriptor: | meta cleavage compound hydrolase | | Authors: | Habe, H, Morii, K, Fushinobu, S, Nam, J.W, Ayabe, Y, Yoshida, T, Wakagi, T, Yamane, H, Nojiri, H, Omori, T. | | Deposit date: | 2002-12-05 | | Release date: | 2003-06-17 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme).
Biochem.Biophys.Res.Commun., 303, 2003
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1D8J
 | | SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA | | Descriptor: | GENERAL TRANSCRIPTION FACTOR TFIIE-BETA | | Authors: | Okuda, M, Watanabe, Y, Okamura, H, Hanaoka, F, Ohkuma, Y, Nishimura, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1999-10-25 | | Release date: | 2000-04-26 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
EMBO J., 19, 2000
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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: | 2024-12-25 | | 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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1D8K
 | | SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA | | Descriptor: | GENERAL TRANSCRIPTION FACTOR TFIIE-BETA | | Authors: | Okuda, M, Watanabe, Y, Okamura, H, Hanaoka, F, Ohkuma, Y, Nishimura, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1999-10-25 | | Release date: | 2000-04-26 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
EMBO J., 19, 2000
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8GST
 | | Crystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (pyruvate bound-form) | | Descriptor: | L-2,4-diketo-3-deoxyrhamnonate hydrolase, MAGNESIUM ION, PYRUVIC ACID | | Authors: | Fukuhara, S, Watanabe, Y, Watanabe, S, Nishiwaki, H. | | Deposit date: | 2022-09-07 | | Release date: | 2023-02-08 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.71 Å) | | Cite: | Crystal Structure of l-2,4-Diketo-3-deoxyrhamnonate Hydrolase Involved in the Nonphosphorylated l-Rhamnose Pathway from Bacteria.
Biochemistry, 62, 2023
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8GSR
 | | Crystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (apo-form) | | Descriptor: | L-2,4-diketo-3-deoxyrhamnonate hydrolase, MAGNESIUM ION | | Authors: | Fukuhara, S, Watanabe, Y, Watanabe, S, Nishiwaki, H. | | Deposit date: | 2022-09-07 | | Release date: | 2023-02-08 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.73 Å) | | Cite: | Crystal Structure of l-2,4-Diketo-3-deoxyrhamnonate Hydrolase Involved in the Nonphosphorylated l-Rhamnose Pathway from Bacteria.
Biochemistry, 62, 2023
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6HJ4
 | | Crystal structure of Whitewater Arroyo virus GP1 glycoprotein at pH 7.5 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CADMIUM ION, Pre-glycoprotein polyprotein GP complex | | Authors: | Pryce, R, Ng, W.M, Zeltina, A, Watanabe, Y, El Omari, K, Wagner, A, Bowden, T.A. | | Deposit date: | 2018-08-31 | | Release date: | 2018-10-10 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.43 Å) | | Cite: | Structure-Based Classification Defines the Discrete Conformational Classes Adopted by the Arenaviral GP1.
J. Virol., 93, 2019
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3WAH
 | | Crystal Structure of HasAp with Iron MesoporphyrinIX | | Descriptor: | Heme acquisition protein HasAp, Mesoheme | | Authors: | Shirataki, C, Shoji, O, Sugimoto, H, Shiro, Y, Watanabe, Y. | | Deposit date: | 2013-05-02 | | Release date: | 2014-01-29 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Inhibition of Heme Uptake in Pseudomonas aeruginosa by its Hemophore (HasAp ) Bound to Synthetic Metal Complexes
Angew.Chem.Int.Ed.Engl., 53, 2014
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1J3F
 | | Crystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me2-salophen)/apo-A71G Myoglobin | | Descriptor: | 'N,N'-BIS-(2-HYDROXY-3-METHYL-BENZYLIDENE)-BENZENE-1,2-DIAMINE', CHROMIUM ION, Myoglobin, ... | | Authors: | Koshiyama, T, Kono, M, Ohashi, M, Ueno, T, Suzuki, A, Yamane, T, Watanabe, Y. | | Deposit date: | 2003-01-24 | | Release date: | 2004-05-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Coordinated Design of Cofactor and Active Site Structures in Development of New Protein Catalysts
J.Am.Chem.Soc., 127, 2005
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8W9G
 | | Hepatitis B virus core protein Y132A mutant in complex with CBT-078 | | Descriptor: | 2-fluoranyl-N1-(4-fluorophenyl)-N3-(2-methylphenyl)benzene-1,3-dicarboxamide, Capsid protein | | Authors: | Iwasaki, W, Katsura, K, Tomabechi, Y, Niwa, H, Ogawa, K, Kojima, S, Shirouzu, M. | | Deposit date: | 2023-09-05 | | Release date: | 2024-09-11 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Screening systems for the detection of hepatitis B virus replication and capsid assembly
To Be Published
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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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7Y9P
 | | Xylitol dehydrogenase S96C/S99C/Y102C mutant(thermostabilized form) from Pichia stipitis | | Descriptor: | DI(HYDROXYETHYL)ETHER, GLYCEROL, SULFATE ION, ... | | Authors: | Yoshiwara, K, Watanabe, Y, Watanabe, S. | | Deposit date: | 2022-06-25 | | Release date: | 2023-02-15 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass.
Sci Rep, 13, 2023
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