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6R8Z
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BU of 6r8z by Molmil
Cryo-EM structure of NCP_THF2(-1)-UV-DDB
Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
6R94
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BU of 6r94 by Molmil
Cryo-EM structure of NCP_THF2(-3)
Descriptor: Histone H2A type 1-B/E, Histone H2B type 1-J, Histone H3.1, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
6R90
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BU of 6r90 by Molmil
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4.5 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
6R91
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BU of 6r91 by Molmil
Cryo-EM structure of NCP_THF2(-3)-UV-DDB
Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
6R92
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BU of 6r92 by Molmil
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B
Descriptor: DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4.8 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
6R8Y
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BU of 6r8y by Molmil
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB
Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4.3 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
6R93
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BU of 6r93 by Molmil
Cryo-EM structure of NCP-6-4PP
Descriptor: Histone H2A type 1-B/E, Histone H2B type 1-J, Histone H3.1, ...
Authors:Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H.
Deposit date:2019-04-02
Release date:2019-06-12
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (4 Å)
Cite:DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
5GMY
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BU of 5gmy by Molmil
Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) tethered with an acceptor peptide containing the NVT sequon via a disulfide bond
Descriptor: MAGNESIUM ION, Transmembrane oligosaccharyl transferase, putative, ...
Authors:Matsumoto, S, Kohda, D.
Deposit date:2016-07-18
Release date:2017-02-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Tethering an N-Glycosylation Sequon-Containing Peptide Creates a Catalytically Competent Oligosaccharyltransferase Complex
Biochemistry, 56, 2017
3VGP
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BU of 3vgp by Molmil
Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AF_0329) from Archaeoglobus fulgidus
Descriptor: Transmembrane oligosaccharyl transferase, putative
Authors:Matsumoto, S, Igura, M, Nyirenda, J, Yuzawa, S, Noda, N.N, Inagaki, F, Kohda, D.
Deposit date:2011-08-18
Release date:2012-07-04
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A Resolution
Biochemistry, 51, 2012
2E5E
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BU of 2e5e by Molmil
Solution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts
Descriptor: Advanced glycosylation end product-specific receptor
Authors:Matsumoto, S, Yoshida, T, Yasumatsu, I, Yamamoto, H, Kobayashi, Y, Ohkubo, T.
Deposit date:2006-12-20
Release date:2007-12-25
Last modified:2022-03-09
Method:SOLUTION NMR
Cite:Solution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts
to be published
5ZC6
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BU of 5zc6 by Molmil
Solution structure of H-RasT35S mutant protein in complex with KBFM123
Descriptor: 3-oxidanyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]naphthalene-2-carboxamide, GTPase HRas, MAGNESIUM ION, ...
Authors:Matsumoto, S, Hayashi, Y, Hiraga, T, Matsuo, K, Kataoka, T.
Deposit date:2018-02-15
Release date:2018-09-12
Last modified:2018-09-26
Method:SOLUTION NMR
Cite:Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring
Biochemistry, 57, 2018
3VW8
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BU of 3vw8 by Molmil
Crystal structure of human c-Met kinase domain with its inhibitor
Descriptor: CHLORIDE ION, Hepatocyte growth factor receptor, N-({4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}carbamothioyl)-2-phenylacetamide
Authors:Matsumoto, S, Miyamoto, N, Hirayama, T, Oki, H, Okada, K, Tawada, M, Iwata, H, Miki, H, Nakamura, K, Hori, A, Imamura, S.
Deposit date:2012-08-08
Release date:2013-08-14
Last modified:2022-08-24
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structure-based design, synthesis, and evaluation of imidazo[1,2-b]pyridazine and imidazo[1,2-a]pyridine derivatives as novel dual c-Met and VEGFR2 kinase inhibitors.
Bioorg.Med.Chem., 21, 2013
3WAJ
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BU of 3waj by Molmil
Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) complex with Zn and sulfate
Descriptor: SULFATE ION, Transmembrane oligosaccharyl transferase, ZINC ION
Authors:Matsumoto, S, Shimada, A, Kohda, D.
Deposit date:2013-05-03
Release date:2013-10-30
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.501 Å)
Cite:Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation
Proc.Natl.Acad.Sci.USA, 110, 2013
3WAK
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BU of 3wak by Molmil
Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) in the apo form
Descriptor: MANGANESE (II) ION, Transmembrane oligosaccharyl transferase
Authors:Matsumoto, S, Shimada, A, Kohda, D.
Deposit date:2013-05-03
Release date:2013-10-30
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.413 Å)
Cite:Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation
Proc.Natl.Acad.Sci.USA, 110, 2013
3WAI
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BU of 3wai by Molmil
Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AfAglB-L, O29867_ARCFU) from Archaeoglobus fulgidus as a MBP fusion
Descriptor: Maltose-binding periplasmic protein, Transmembrane oligosaccharyl transferase
Authors:Matsumoto, S, Shimada, A, Kohda, D.
Deposit date:2013-05-03
Release date:2013-07-17
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.897 Å)
Cite:Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases
Bmc Struct.Biol., 13, 2013
5B30
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BU of 5b30 by Molmil
H-Ras WT in complex with GppNHp (state 1) after structural transition by humidity control
Descriptor: CALCIUM ION, GTPase HRas, MAGNESIUM ION, ...
Authors:Kumasaka, T, Miyano, N, Baba, S, Matsumoto, S, Kataoka, T, Shima, F.
Deposit date:2016-02-08
Release date:2016-06-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep, 6, 2016
5B2Z
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BU of 5b2z by Molmil
H-Ras WT in complex with GppNHp (state 2*) before structural transition by humidity control
Descriptor: CALCIUM ION, GTPase HRas, MAGNESIUM ION, ...
Authors:Kumasaka, T, Miyano, N, Baba, S, Matsumoto, S, Kataoka, T, Shima, F.
Deposit date:2016-02-07
Release date:2016-06-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal
Sci Rep, 6, 2016
5X9S
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BU of 5x9s by Molmil
Crystal structure of fully modified H-Ras-GppNHp
Descriptor: CALCIUM ION, GTPase HRas, MAGNESIUM ION, ...
Authors:Matsumoto, S, Ke, H, Murashima, Y, Taniguchi-Tamura, H, Miyamoto, R, Yoshikawa, Y, Kumasaka, T, Mizohata, E, Edamatsu, H, Kataoka, T.
Deposit date:2017-03-09
Release date:2017-08-30
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for intramolecular interaction of post-translationally modified H-RasGTP prepared by protein ligation
FEBS Lett., 591, 2017
7DPJ
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BU of 7dpj by Molmil
H-Ras Q61L in complex with GppNHp (state 1) after structural transition by humidity control
Descriptor: CALCIUM ION, GTPase HRas, MAGNESIUM ION, ...
Authors:Taniguchi, H, Matsumoto, S, Miyamoto, R, Kawamura, T, Kumasaka, T, Kataoka, T.
Deposit date:2020-12-19
Release date:2021-07-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.976 Å)
Cite:Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein.
Biochem.Biophys.Res.Commun., 565, 2021
7DPH
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BU of 7dph by Molmil
H-Ras Q61H in complex with GppNHp (state 1) after structural transition by humidity control
Descriptor: GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, ...
Authors:Taniguchi, H, Matsumoto, S, Kawamura, T, Kumasaka, T, Kataoka, T.
Deposit date:2020-12-19
Release date:2021-07-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein.
Biochem.Biophys.Res.Commun., 565, 2021
4YM6
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BU of 4ym6 by Molmil
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
4YM5
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BU of 4ym5 by Molmil
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
5TNT
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BU of 5tnt by Molmil
Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors
Descriptor: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, Coagulation factor IX, N-[(1S,4S,7R)-2-(3-amino-4-chloro[1,2]oxazolo[5,4-c]pyridin-7-yl)-2-azabicyclo[2.2.1]heptan-7-yl]-2-chloro-4-(3-methyl-1H-1,2,4-triazol-1-yl)benzamide, ...
Authors:Sakurada, I, Endo, T, Hikita, K, Hirabayashi, T, Hosaka, Y, Kato, Y, Maeda, Y, Matsumoto, S, Mizuno, T, Nagasue, A, Nishimura, T, Shimada, S, Shinozaki, M, Taguchi, K, Takeuchi, K, Yokoyama, T, Hruza, A, Reichert, P, Zhang, T, Wood, H.B, Nakao, K, Furusako, S.
Deposit date:2016-10-14
Release date:2017-04-26
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors.
Bioorg. Med. Chem. Lett., 27, 2017
5TNO
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BU of 5tno by Molmil
Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors
Descriptor: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, Coagulation factor IX, SODIUM ION, ...
Authors:Sakurada, I, Endo, T, Hikita, K, Hirabayashi, T, Hosaka, Y, Kato, Y, Maeda, Y, Matsumoto, S, Mizuno, T, Nagasue, H, Nishimura, T, Shimada, S, Shinozaki, M, Taguchi, K, Takeuchi, K, Yokoyama, T, Hruza, A, Reichert, P, Zhang, T, Wood, H.B, Nakao, K, Furusako, S.
Deposit date:2016-10-14
Release date:2017-04-26
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors.
Bioorg. Med. Chem. Lett., 27, 2017
3VU0
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BU of 3vu0 by Molmil
Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AfAglB-S2, AF_0040, O30195_ARCFU) from Archaeoglobus fulgidus
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Putative uncharacterized protein
Authors:Nyirenda, J, Matsumoto, S, Saitoh, T, Maita, N, Noda, N.N, Inagaki, F, Kohda, D.
Deposit date:2012-06-13
Release date:2013-01-23
Last modified:2023-12-06
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Crystallographic and NMR Evidence for Flexibility in Oligosaccharyltransferases and Its Catalytic Significance
Structure, 21, 2013

 

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