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PDB: 2087 件
3UG1
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Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in the apo form
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Epidermal growth factor receptor
著者Parker, L.J, Handa, N, Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Yokoyama, S.
登録日2011-11-02
公開日2012-03-07
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 32, 2013
5B48
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2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai
分子名称: 2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-(1-oxidanylpropylidene)-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate, 2-oxoacid--ferredoxin oxidoreductase alpha subunit, 2-oxoacid--ferredoxin oxidoreductase beta subunit, ...
著者Yan, Z, Maruyama, A, Arakawa, T, Fushinobu, S, Wakagi, T.
登録日2016-04-01
公開日2016-09-28
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii
Sci Rep, 6, 2016
5BXP
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LNBase in complex with LNB-LOGNAc
分子名称: Lacto-N-biosidase, SULFATE ION, beta-D-galactopyranose-(1-3)-N-acetylglucosaminono-1,5-lactone (Z)-oxime
著者Ito, T, Arakawa, T, Fushinobu, S.
登録日2015-06-09
公開日2015-09-09
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis
Chem.Commun.(Camb.), 51, 2015
6KQT
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Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - native protein
分子名称: SODIUM ION, TRIETHYLENE GLYCOL, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Yamada, C, Arakawa, T, Pichler, M.J, Abou Hachem, M, Fushinobu, S.
登録日2019-08-18
公開日2020-06-10
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways.
Nat Commun, 11, 2020
6KQS
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Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - selenomethionine derivative
分子名称: GLYCEROL, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, lacto-N-biosidase
著者Yamada, C, Arakawa, T, Pichler, M.J, Abou Hachem, M, Fushinobu, S.
登録日2019-08-18
公開日2020-06-10
最終更新日2020-07-29
実験手法X-RAY DIFFRACTION (1.4 Å)
主引用文献Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways.
Nat Commun, 11, 2020
3AG4
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Bovine Heart Cytochrome c Oxidase in the Cyanide Ion-bound Fully Reduced State at 100 K
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Muramoto, K, Ohta, K, Shinzawa-Itoh, K, Kanda, K, Taniguchi, M, Nabekura, H, Yamashita, E, Tsukihara, T, Yoshikawa, S.
登録日2010-03-19
公開日2010-04-28
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate
Proc.Natl.Acad.Sci.USA, 107, 2010
3A99
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Structure of PIM-1 kinase crystallized in the presence of P27KIP1 Carboxy-terminal peptide
分子名称: MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Proto-oncogene serine/threonine-protein kinase pim-1
著者Morishita, D, Takami, M, Yoshikawa, S, Katayama, R, Sato, S, Kukimoto-Niino, M, Umehara, T, Shirouzu, M, Sekimizu, K, Yokoyama, S, Fujita, N.
登録日2009-10-22
公開日2010-11-03
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Cell-permeable carboxyl-terminal p27(Kip1) peptide exhibits anti-tumor activity by inhibiting Pim-1 kinase
J.Biol.Chem., 286, 2011
3ABM
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Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset)
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S.
登録日2009-12-16
公開日2010-01-19
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
4JAW
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Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline
分子名称: 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL, Lacto-N-biosidase, SULFATE ION, ...
著者Ito, T, Katayama, T, Stubbs, K.A, Fushinobu, S.
登録日2013-02-19
公開日2013-03-20
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
J.Biol.Chem., 288, 2013
2ZXW
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Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset)
分子名称: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
著者Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Hirata, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S.
登録日2009-01-08
公開日2009-02-24
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
2D9S
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BU of 2d9s by Molmil
Solution structure of RSGI RUH-049, a UBA domain from mouse cDNA
分子名称: CBL E3 ubiquitin protein ligase
著者Hamada, T, Hirota, H, Lin, Y.-J, Guntert, P, Kurosaki, C, Izumi, K, Yoshida, M, Koshiba, S, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2005-12-13
公開日2007-01-23
最終更新日2024-05-29
実験手法SOLUTION NMR
主引用文献Solution structure of RSGI RUH-049, a UBA domain from mouse cDNA
To be Published
4JJF
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BU of 4jjf by Molmil
Crystal structure of FE-hydrogenase from methanothermobacter marburgensis in complex with 2-naphthylisocyanide
分子名称: 5,10-methenyltetrahydromethanopterin hydrogenase, N-(naphthalen-2-yl)methanimine, iron-guanylyl pyridinol cofactor
著者Tamura, H, Warkentin, E, Ermler, U, Shima, S.
登録日2013-03-07
公開日2013-08-07
最終更新日2023-09-20
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Crystal structures of [fe]-hydrogenase in complex with inhibitory isocyanides: implications for the h2 -activation site.
Angew.Chem.Int.Ed.Engl., 52, 2013
4ZLG
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BU of 4zlg by Molmil
Cellobionic acid phosphorylase - gluconic acid complex
分子名称: CHLORIDE ION, D-gluconic acid, D-glucono-1,5-lactone, ...
著者Nam, Y.W, Arakawa, T, Fushinobu, S.
登録日2015-05-01
公開日2015-06-10
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes.
J.Biol.Chem., 290, 2015
2Z0W
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BU of 2z0w by Molmil
Crystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a swapped-dimer
分子名称: CAP-Gly domain-containing linker protein 4
著者Saito, K, Yoshikawa, S, Nishino, A, Murayama, K, Terada, T, Shirouzu, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2007-05-07
公開日2007-11-13
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Crystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a swapped-dimer
To be Published
2Z13
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BU of 2z13 by Molmil
Crystal structure of the N-terminal DUF1126 in human EF-hand domain
分子名称: EF-hand domain-containing family member C2
著者Saito, K, Kishishita, S, Nishino, A, Murayama, K, Terada, T, Shirouzu, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2007-05-07
公開日2007-11-13
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (1.84 Å)
主引用文献Crystal structure of the N-terminal DUF1126 in human EF-hand domain
To be Published
2Z15
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Crystal structure of human Tob1 protein
分子名称: Protein Tob1
著者Saito, K, Kishishita, S, Nishino, A, Murayama, K, Terada, T, Shirouzu, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2007-05-08
公開日2007-11-13
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Crystal structure of human Tob1 protein
To be Published
3VM6
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Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate
分子名称: 1,5-di-O-phosphono-alpha-D-ribofuranose, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
著者Nakamura, A, Fujihashi, M, Aono, R, Sato, T, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K.
登録日2011-12-08
公開日2012-04-25
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1
J.Biol.Chem., 287, 2012
1IO1
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BU of 1io1 by Molmil
CRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN
分子名称: PHASE 1 FLAGELLIN
著者Samatey, F.A, Imada, K, Nagashima, S, Vondervisz, F, Kumasaka, T, Yamamoto, M, Namba, K.
登録日2000-12-28
公開日2001-04-04
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling
Nature, 410, 2001
1UEQ
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Solution Structure of The First PDZ domain of Human Atrophin-1 Interacting Protein 1 (KIAA0705 protein)
分子名称: MEMBRANE ASSOCIATED GUANYLATE KINASE INVERTED-2 (MAGI-2)
著者Zhao, C, Kigawa, T, Tochio, N, Koshiba, S, Inoue, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2003-05-20
公開日2003-11-20
最終更新日2023-12-27
実験手法SOLUTION NMR
主引用文献Solution Structure of The First PDZ domain of Human Atrophin-1 Interacting Protein 1 (KIAA0705 protein)
To be Published
1UEP
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Solution Structure of The Third PDZ Domain of Human Atrophin-1 Interacting Protein 1 (KIAA0705 Protein)
分子名称: Membrane Associated Guanylate Kinase Inverted-2 (MAGI-2)
著者Miyamoto, K, Kigawa, T, Koshiba, S, Inoue, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2003-05-20
公開日2003-11-20
最終更新日2023-12-27
実験手法SOLUTION NMR
主引用文献Solution Structure of The Third PDZ Domain of Human Atrophin-1 Interacting Protein 1 (KIAA0705 Protein)
To be Published
2RQR
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BU of 2rqr by Molmil
The solution structure of human DOCK2 SH3 domain - ELMO1 peptide chimera complex
分子名称: Engulfment and cell motility protein 1,Dedicator of cytokinesis protein 2
著者Yokoyama, S, Tochio, N, Koshiba, S, Kigawa, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2009-10-21
公開日2010-10-27
最終更新日2024-05-01
実験手法SOLUTION NMR
主引用文献Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proc.Natl.Acad.Sci.USA, 109, 2012
3VUO
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BU of 3vuo by Molmil
Crystal structure of nontoxic nonhemagglutinin subcomponent (NTNHA) from clostridium botulinum serotype D strain 4947
分子名称: NTNHA
著者Sagane, Y, Miyashita, S.-I, Miyata, K, Matsumoto, T, Inui, K, Hayashi, S, Suzuki, T, Hasegawa, K, Yajima, S, Yamano, A, Niwa, K, Watanabe, T.
登録日2012-07-03
公開日2012-09-19
実験手法X-RAY DIFFRACTION (3.9 Å)
主引用文献Small-angle X-ray scattering reveals structural dynamics of the botulinum neurotoxin associating protein, nontoxic nonhemagglutinin
Biochem.Biophys.Res.Commun., 425, 2012
2ROZ
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BU of 2roz by Molmil
Structure of the C-terminal PID Domain of Fe65L1 Complexed with the Cytoplasmic Tail of APP Reveals a Novel Peptide Binding Mode
分子名称: Amyloid beta A4 precursor protein-binding family B member 2, peptide from Amyloid beta A4 protein
著者Li, H, Koshiba, S, Tochio, N, Watanabe, S, Harada, T, Inoue, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2008-04-25
公開日2008-07-22
最終更新日2024-05-29
実験手法SOLUTION NMR
主引用文献Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode
J.Biol.Chem., 283, 2008
3VHX
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BU of 3vhx by Molmil
The crystal structure of Arf6-MKLP1 (Mitotic kinesin-like protein 1) complex
分子名称: ADP-ribosylation factor 6, GLYCEROL, GUANOSINE-5'-TRIPHOSPHATE, ...
著者Makyio, H, Takei, T, Ohgi, H, Takahashi, S, Takatsu, H, Ueda, T, Kanaho, Y, Xie, Y, Shin, H.W, Kamikubo, H, Kataoka, M, Kawasaki, M, Kato, R, Wakatsuki, S, Nakayama, K.
登録日2011-09-12
公開日2012-05-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.81 Å)
主引用文献Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis
Embo J., 31, 2012
6J9S
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Penta mutant of Lactobacillus casei lactate dehydrogenase
分子名称: GLYCEROL, L-lactate dehydrogenase, SULFATE ION
著者Arai, K, Miyanaga, A, Uchikoba, H, Fushinobu, S, Taguchi, H.
登録日2019-01-24
公開日2019-02-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structure of penta mutant of L-lactate dehydrogenase from Lactobacillus casei
To Be Published

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