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PDB: 138 results

1UH3
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Thermoactinomyces vulgaris R-47 alpha-amylase/acarbose complex
Descriptor: (1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol, 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose, 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL, ...
Authors:Abe, A, Tonozuka, T, Sakano, Y, Kamitori, S.
Deposit date:2003-06-23
Release date:2004-01-13
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Complex Structures of Thermoactinomyces vulgaris R-47 alpha-Amylase 1 with Malto-oligosaccharides Demonstrate the Role of Domain N Acting as a Starch-binding Domain
J.Mol.Biol., 335, 2004
1UH4
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Thermoactinomyces vulgaris R-47 alpha-amylase 1/malto-tridecaose complex
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, alpha-D-glucopyranose, ...
Authors:Abe, A, Tonozuka, T, Sakano, Y, Kamitori, S.
Deposit date:2003-06-24
Release date:2004-01-13
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Complex Structures of Thermoactinomyces vulgaris R-47 alpha-Amylase 1 with Malto-oligosaccharides Demonstrate the Role of Domain N Acting as a Starch-binding Domain
J.Mol.Biol., 335, 2004
1UH2
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Thermoactinomyces vulgaris R-47 alpha-amylase/malto-hexaose complex
Descriptor: CALCIUM ION, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ...
Authors:Abe, A, Tonozuka, T, Sakano, Y, Kamitori, S.
Deposit date:2003-06-23
Release date:2004-01-13
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2 Å)
Cite:Complex Structures of Thermoactinomyces vulgaris R-47 alpha-Amylase 1 with Malto-oligosaccharides Demonstrate the Role of Domain N Acting as a Starch-binding Domain
J.Mol.Biol., 335, 2004
2ZKN
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X-ray structure of mutant galectin-1/lactose complex
Descriptor: Galectin-1, beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
Authors:Abe, A, Yoshida, H, Kamitori, S.
Deposit date:2008-03-26
Release date:2008-09-30
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Functional and structural bases of a cysteine-less mutant as a long-lasting substitute for galectin-1
Glycobiology, 18, 2008
2D0H
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Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ...
Authors:Abe, A, Yoshida, H, Tonozuka, T, Sakano, Y, Kamitori, S.
Deposit date:2005-08-02
Release date:2006-07-11
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages
Febs J., 272, 2005
2D0F
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Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose, ...
Authors:Abe, A, Yoshida, H, Tonozuka, T, Sakano, Y, Kamitori, S.
Deposit date:2005-08-02
Release date:2006-07-11
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages
Febs J., 272, 2005
2D0G
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Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P5, a pullulan model oligosaccharide
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, alpha-D-glucopyranose, ...
Authors:Abe, A, Yoshida, H, Tonozuka, T, Sakano, Y, Kamitori, S.
Deposit date:2005-08-02
Release date:2006-07-11
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages
Febs J., 272, 2005
2XQ2
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Structure of the K294A mutant of vSGLT
Descriptor: DI(HYDROXYETHYL)ETHER, SODIUM/GLUCOSE COTRANSPORTER
Authors:Watanabe, A, Choe, S, Chaptal, V, Rosenberg, J.M, Wright, E.M, Grabe, M, Abramson, J.
Deposit date:2010-09-01
Release date:2010-12-08
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (2.73 Å)
Cite:The Mechanism of Sodium and Substrate Release from the Binding Pocket of Vsglt
Nature, 468, 2010
8J92
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Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W
Descriptor: DNA (169-MER), HTA6, HTB9, ...
Authors:Osakabe, A, Takizawa, Y, Horikoshi, N, Hatazawa, S, Berger, F, Kurumizaka, H, Kakutani, T.
Deposit date:2023-05-02
Release date:2024-07-03
Last modified:2024-07-24
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun, 15, 2024
8J91
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Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones
Descriptor: DNA (169-MER), HTA13, Histone H2B.6, ...
Authors:Osakabe, A, Takizawa, Y, Horikoshi, N, Hatazawa, S, Berger, F, Kurumizaka, H, Kakutani, T.
Deposit date:2023-05-02
Release date:2024-07-03
Last modified:2024-07-24
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun, 15, 2024
8J90
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Cryo-EM structure of DDM1-nucleosome complex
Descriptor: ATP-dependent DNA helicase DDM1, DNA (169-MER), HTA6, ...
Authors:Osakabe, A, Takizawa, Y, Horikoshi, N, Hatazawa, S, Berger, F, Kurumizaka, H, Kakutani, T.
Deposit date:2023-05-02
Release date:2024-07-03
Last modified:2024-07-24
Method:ELECTRON MICROSCOPY (4.71 Å)
Cite:Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Nat Commun, 15, 2024
5JRG
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Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)
Descriptor: CHLORIDE ION, DNA (145-MER), Histone H2A type 1-B/E, ...
Authors:Osakabe, A, Arimura, Y, Horikoshi, N, Kurumizaka, H.
Deposit date:2016-05-06
Release date:2017-03-08
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Polymorphism of apyrimidinic DNA structures in the nucleosome
Sci Rep, 7, 2017
8R67
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tubulin-cryptophycin complex
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-[(3~{S},10~{R},13~{E},16~{S})-10-[(3-chloranyl-4-methoxy-phenyl)methyl]-6,6-dimethyl-2,5,9,12-tetrakis(oxidanylidene)-16-[(1~{S})-1-[(2~{R},3~{R})-3-phenyloxiran-2-yl]ethyl]-1,4-dioxa-8,11-diazacyclohexadec-13-en-3-yl]ethanoic acid, CALCIUM ION, ...
Authors:Abel, A.C, Muehlethaler, T, Dessin, C, Steinmetz, M.O, Sewald, N, Prota, A.E.
Deposit date:2023-11-21
Release date:2024-05-22
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Bridging the maytansine and vinca sites: Cryptophycins target beta-tubulin's T5-loop.
J.Biol.Chem., 300, 2024
5CPJ
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Nucleosome containing methylated Sat2R DNA
Descriptor: DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H.
Deposit date:2015-07-21
Release date:2015-10-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.15 Å)
Cite:Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.
Open Biology, 5, 2015
5CPI
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Nucleosome containing unmethylated Sat2R DNA
Descriptor: DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H.
Deposit date:2015-07-21
Release date:2015-10-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.902 Å)
Cite:Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.
Open Biology, 5, 2015
5CPK
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Nucleosome containing methylated Sat2L DNA
Descriptor: DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H.
Deposit date:2015-07-21
Release date:2015-10-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.632 Å)
Cite:Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.
Open Biology, 5, 2015
8B9R
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Molecular structure of Cu(II)-bound amyloid-beta monomer implicated in inhibition of peptide self-assembly in Alzheimer's disease
Descriptor: Amyloid-beta A4 protein, COPPER (II) ION
Authors:Abelein, A, Ciofi-Baffoni, S, Morman, C, Kumar, R, Giachetti, A, Piccioli, M, Biverstal, H.
Deposit date:2022-10-06
Release date:2023-02-01
Last modified:2024-06-19
Method:SOLUTION NMR
Cite:Molecular Structure of Cu(II)-Bound Amyloid-beta Monomer Implicated in Inhibition of Peptide Self-Assembly in Alzheimer's Disease.
Jacs Au, 2, 2022
8B9Q
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Molecular structure of Cu(II)-bound amyloid-beta monomer implicated in inhibition of peptide self-assembly in Alzheimer's disease
Descriptor: Amyloid-beta A4 protein, COPPER (II) ION
Authors:Abelein, A, Ciofi-Baffoni, S, Kumar, R, Giachetti, A, Piccioli, M, Biverstal, H.
Deposit date:2022-10-06
Release date:2023-02-08
Last modified:2024-06-05
Method:SOLUTION NMR
Cite:Molecular Structure of Cu(II)-Bound Amyloid-beta Monomer Implicated in Inhibition of Peptide Self-Assembly in Alzheimer's Disease.
Jacs Au, 2, 2022
4YM5
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Crystal structure of the human nucleosome containing 6-4PP (inside)
Descriptor: 144 mer-DNA, 144-mer DNA, Histone H2A type 1-B/E, ...
Authors:Osakabe, A, Tachiwana, H, Kagawa, W, Horikoshi, N, Matsumoto, S, Hasegawa, M, Matsumoto, N, Toga, T, Yamamoto, J, Hanaoka, F, Thoma, N.H, Sugasawa, K, Iwai, S, Kurumizaka, H.
Deposit date:2015-03-06
Release date:2015-12-02
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (4.005 Å)
Cite:Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome
Sci Rep, 5, 2015
4YM6
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Crystal structure of the human nucleosome containing 6-4PP (outside)
Descriptor: 145-MER DNA, Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Osakabe, A, Tachiwana, H, Kagawa, W, Horikoshi, N, Matsumoto, S, Hasegawa, M, Matsumoto, N, Toga, T, Yamamoto, J, Hanaoka, F, Thoma, N.H, Sugasawa, K, Iwai, S, Kurumizaka, H.
Deposit date:2015-03-06
Release date:2015-12-02
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.514 Å)
Cite:Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome
Sci Rep, 5, 2015
1L6G
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Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine
Descriptor: N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE, alanine racemase
Authors:Watanabe, A, Yoshimura, T, Mikami, B, Hayashi, H, Kagamiyama, H, Esaki, N.
Deposit date:2002-03-10
Release date:2002-06-05
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.
J.Biol.Chem., 277, 2002
1L6F
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Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine
Descriptor: ALANYL-PYRIDOXAL-5'-PHOSPHATE, alanine racemase
Authors:Watanabe, A, Yoshimura, T, Mikami, B, Hayashi, H, Kagamiyama, H, Esaki, N.
Deposit date:2002-03-09
Release date:2002-06-05
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.
J.Biol.Chem., 277, 2002
1RNR
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AUTOCATALYTIC GENERATION OF DOPA IN THE ENGINEERED PROTEIN R2 F208Y FROM ESCHERICHIA COLI RIBONUCLEOTIDE REDUCTASE AND CRYSTAL STRUCTURE OF THE DOPA-208 PROTEIN
Descriptor: FE (III) ION, MERCURY (II) ION, RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
Authors:Aberg, A, Nordlund, P.
Deposit date:1993-04-26
Release date:1994-01-31
Last modified:2017-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Autocatalytic generation of dopa in the engineered protein R2 F208Y from Escherichia coli ribonucleotide reductase and crystal structure of the dopa-208 protein.
Biochemistry, 32, 1993
2GS9
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Crystal structure of TT1324 from Thermus thermophilis HB8
Descriptor: FORMIC ACID, Hypothetical protein TT1324, S-ADENOSYL-L-HOMOCYSTEINE
Authors:Kamitori, S, Abe, A, Ebihara, A, Kanagawa, M, Nakagawa, N, Kuroishi, C, Agari, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2006-04-25
Release date:2007-03-13
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structure of TT1324 from Thermus thermophilis HB8
To be Published
1JI2
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Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha-Amylase 2
Descriptor: ALPHA-AMYLASE II, CALCIUM ION
Authors:Kamitori, S, Abe, A, Ohtaki, A, Kaji, A, Tonozuka, T, Sakano, Y.
Deposit date:2001-06-28
Release date:2002-06-05
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.
J.Mol.Biol., 318, 2002

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