1V3Y
 
 | | The crystal structure of peptide deformylase from Thermus thermophilus HB8 | | Descriptor: | Peptide deformylase | | Authors: | Kamo, M, Kudo, N, Lee, W.C, Ito, K, Motoshim, H, Tanokura, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-11-07 | | Release date: | 2004-12-28 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | The crystal structure of peptide deformylase from Thermus thermophilus HB8
to be published
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5Y9Z
 | | Crystal structure of rat hematopoietic prostaglandin D synthase | | Descriptor: | 1,2-ETHANEDIOL, 1,4-DIETHYLENE DIOXIDE, GLUTATHIONE, ... | | Authors: | Kamo, M, Furubayashi, N, Inaka, K, Tanaka, H, Aritake, K, Urade, Y. | | Deposit date: | 2017-08-29 | | Release date: | 2018-09-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.09 Å) | | Cite: | Crystal structure of rat hematopoietic prostaglandin D synthase
To Be Published
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9KKU
 | | Helix-loop-helix peptide (M49) in complex with VEGF-A | | Descriptor: | M49, Vascular endothelial growth factor A, long form | | Authors: | Kamo, M, Michigami, M, Inaka, K, Furubayashi, N, Kaito, S, Kobayashi, Y, Shinohara, Y, Fujii, I. | | Deposit date: | 2024-11-14 | | Release date: | 2024-12-11 | | Method: | X-RAY DIFFRACTION (1.46 Å) | | Cite: | Structural Insights into Helix-Loop-Helix Peptides for "Ligand-Targeting" Intracellular Drug Delivery via VEGF Receptor-Mediated Endocytosis.
Biochem.Biophys.Res.Commun., 741, 2024
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9JU1
 | | Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A | | Descriptor: | SULFATE ION, VS42-LR3, Vascular endothelial growth factor A, ... | | Authors: | Kamo, M, Michigami, M, Inaka, K, Furubayashi, N, Kaito, S, Kobayashi, Y, Shinohara, Y, Fujii, I. | | Deposit date: | 2024-10-07 | | Release date: | 2024-12-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural insights into molecular-targeting helix-loop-helix peptide against vascular endothelial growth factor-A.
Biochem Biophys Res Commun, 734, 2024
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5YWE
 | | Crystal structure of hematopoietic prostaglandin D synthase apo form | | Descriptor: | GLUTATHIONE, GLYCEROL, Hematopoietic prostaglandin D synthase, ... | | Authors: | Kamo, M, Furubayashi, N, Inaka, K, Aritake, K, Urade, Y. | | Deposit date: | 2017-11-29 | | Release date: | 2018-12-05 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Crystal structure of hematopoietic prostaglandin D synthase apo form
To Be Published
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5YX1
 | | Crystal structure of hematopoietic prostaglandin D synthase in complex with U004 | | Descriptor: | GLUTATHIONE, GLYCEROL, Hematopoietic prostaglandin D synthase, ... | | Authors: | Kamo, M, Furubayashi, N, Inaka, K, Aritake, K, Urade, Y, Takaya, D, Tanaka, A. | | Deposit date: | 2017-12-01 | | Release date: | 2018-12-05 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.39 Å) | | Cite: | Crystal structure of hematopoietic prostaglandin D synthase in complex with U004
To Be Published
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8HAL
 | | Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 | | Descriptor: | CREB-binding protein, DNA (180-mer), Histone H2A type 1-B/E, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-11-20 | | Method: | ELECTRON MICROSCOPY (4.4 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAG
 | | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) | | Descriptor: | DNA (180-mer), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAM
 | | Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 | | Descriptor: | CREB-binding protein, DNA (180-mer), Histone H2A type 1-B/E, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (4.5 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAN
 | | Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 | | Descriptor: | CREB-binding protein, DNA (180-mer), Histone H2A type 1-B/E, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-10-23 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAH
 | | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) | | Descriptor: | DNA (180-mer), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-11-13 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAI
 | | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) | | Descriptor: | DNA (180-mer), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-11-13 | | Method: | ELECTRON MICROSCOPY (4.7 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAJ
 | | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) | | Descriptor: | DNA (180-mer), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (4.8 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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8HAK
 | | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) | | Descriptor: | DNA (180-mer), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2024-11-13 | | Method: | ELECTRON MICROSCOPY (4.5 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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1ZOV
 | | Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129 | | Descriptor: | CHLORIDE ION, FLAVIN-ADENINE DINUCLEOTIDE, Monomeric sarcosine oxidase | | Authors: | Nagata, K, Sasaki, H, Ohtsuka, J, Hua, M, Okai, M, Kubota, K, Kamo, M, Ito, K, Ichikawa, T, Koyama, Y, Tanokura, M. | | Deposit date: | 2005-05-14 | | Release date: | 2006-05-23 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop
PROC.JPN.ACAD.,SER.B, 81, 2005
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3WG8
 | | Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist AS6 | | Descriptor: | (2Z,4E)-5-[(1S)-3-(hexylsulfanyl)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid, Abscisic acid receptor PYR1 | | Authors: | Akiyama, T, Sue, M, Takeuchi, J, Okamoto, M, Muto, T, Endo, A, Nambara, E, Hirai, N, Ohnishi, T, Cutler, S.R, Todoroki, Y, Yajima, S. | | Deposit date: | 2013-07-31 | | Release date: | 2014-05-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Designed abscisic acid analogs as antagonists of PYL-PP2C receptor interactions
Nat.Chem.Biol., 10, 2014
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9L3S
 | | Staphylococcus aureus lipase-Penfluridol complex (in space) | | Descriptor: | 1-[4,4-bis(4-fluorophenyl)butyl]-4-[4-chloranyl-3-(trifluoromethyl)phenyl]piperidin-4-ol, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Kitadokoro, J, Hirokawa, T, Kamo, M, Furubayasi, N, Inaka, K, Kamitani, S, Kitadokoro, K. | | Deposit date: | 2024-12-19 | | Release date: | 2025-04-30 | | Method: | X-RAY DIFFRACTION (2.57 Å) | | Cite: | Structural analysis shows the mode of inhibition for Staphylococcus aureus lipase by antipsychotic penfluridol.
Sci Rep, 15, 2025
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2Z1N
 | | Crystal structure of APE0912 from Aeropyrum pernix K1 | | Descriptor: | SODIUM ION, dehydrogenase | | Authors: | Ichimura, T, Yamamura, A, Mimoto, F, Ohtsuka, J, Miyazono, K, Okai, M, Kamo, M, Lee, W.-C, Nagata, K, Tanokura, M. | | Deposit date: | 2007-05-10 | | Release date: | 2008-03-18 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1
Proteins, 70, 2008
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2D37
 | | The Crystal Structure of Flavin Reductase HpaC complexed with NAD+ | | Descriptor: | FLAVIN MONONUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, hypothetical NADH-dependent FMN oxidoreductase | | Authors: | Okai, M, Kudo, N, Lee, W.C, Kamo, M, Nagata, K, Tanokura, M. | | Deposit date: | 2005-09-26 | | Release date: | 2006-05-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Biochemistry, 45, 2006
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2D36
 | | The Crystal Structure of Flavin Reductase HpaC | | Descriptor: | FLAVIN MONONUCLEOTIDE, hypothetical NADH-dependent FMN oxidoreductase | | Authors: | Okai, M, Kudo, N, Lee, W.C, Kamo, M, Nagata, K, Tanokura, M. | | Deposit date: | 2005-09-26 | | Release date: | 2006-05-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Biochemistry, 45, 2006
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2D38
 | | The Crystal Structure of Flavin Reductase HpaC complexed with NADP+ | | Descriptor: | FLAVIN MONONUCLEOTIDE, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, hypothetical NADH-dependent FMN oxidoreductase | | Authors: | Okai, M, Kudo, N, Lee, W.C, Kamo, M, Nagata, K, Tanokura, M. | | Deposit date: | 2005-09-26 | | Release date: | 2006-05-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Biochemistry, 45, 2006
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2DVY
 | | Crystal structure of restriction endonucleases PabI | | Descriptor: | Restriction endonuclease PabI | | Authors: | Miyazono, K, Watanabe, M, Kamo, M, Sawasaki, T, Nagata, K, Endo, Y, Tanokura, M, Kobayashi, I. | | Deposit date: | 2006-08-01 | | Release date: | 2007-05-08 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Novel protein fold discovered in the PabI family of restriction enzymes
Nucleic Acids Res., 35, 2007
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2D7J
 | | Crystal Structure Analysis of Glutamine Amidotransferase from Pyrococcus horikoshii OT3 | | Descriptor: | GMP synthase [glutamine-hydrolyzing] subunit A | | Authors: | Maruoka, S, Lee, W.C, Kamo, M, Kudo, N, Nagata, K, Tanokura, M. | | Deposit date: | 2005-11-21 | | Release date: | 2006-11-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Crystal structure of glutamine amidotransferase from Pyrococcus horikoshii OT3
PROC.JPN.ACAD.,SER.B, 81, 2005
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5YE4
 | | Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment | | Descriptor: | 1A9D7 L chain, 1A9D7 VH CH1 chain, ZINC ION, ... | | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | | Deposit date: | 2017-09-15 | | Release date: | 2018-08-22 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.799 Å) | | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Epigenetics, 13, 2018
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5YE3
 | | Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment | | Descriptor: | 2A7D9 L chain, 2A7D9 VH CH1 chain, di-acetylated histone H4 | | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | | Deposit date: | 2017-09-15 | | Release date: | 2018-08-22 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Epigenetics, 13, 2018
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