1V55
 
 | | Bovine heart cytochrome c oxidase at the fully reduced state | | Descriptor: | (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, ... | | Authors: | Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S. | | Deposit date: | 2003-11-21 | | Release date: | 2003-12-23 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
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1V54
 | | Bovine heart cytochrome c oxidase at the fully oxidized state | | Descriptor: | (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, ... | | Authors: | Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S. | | Deposit date: | 2003-11-21 | | Release date: | 2003-12-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
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1J2E
 | | Crystal structure of Human Dipeptidyl peptidase IV | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Dipeptidyl peptidase IV | | Authors: | Hiramatsu, H, Kyono, K, Higashiyama, Y, Fukushima, C, Shima, H, Sugiyama, S, Inaka, K, Yamamoto, A, Shimizu, R. | | Deposit date: | 2002-12-30 | | Release date: | 2003-12-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed beta-propeller fold.
Biochem.Biophys.Res.Commun., 302, 2003
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3VU7
 | | Crystal structure of REV1-REV7-REV3 ternary complex | | Descriptor: | DNA polymerase zeta catalytic subunit, DNA repair protein REV1, Mitotic spindle assembly checkpoint protein MAD2B | | Authors: | Kikuchi, S, Hara, K, Shimizu, T, Sato, M, Hashimoto, H. | | Deposit date: | 2012-06-20 | | Release date: | 2012-08-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis of recruitment of DNA polymerase [zeta] by interaction between REV1 and REV7 proteins
J.Biol.Chem., 287, 2012
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5EGE
 | | Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Morita, J, Kano, K, Kato, K, Takita, H, Ishitani, R, Nishimasu, H, Nureki, O, Aoki, J. | | Deposit date: | 2015-10-27 | | Release date: | 2016-03-09 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase
Sci Rep, 6, 2016
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5EGH
 | | Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Morita, J, Kano, K, Kato, K, Takita, H, Ishitani, R, Nishimasu, H, Nureki, O, Aoki, J. | | Deposit date: | 2015-10-27 | | Release date: | 2016-03-09 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.803 Å) | | Cite: | Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase
Sci Rep, 6, 2016
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7YBD
 | | Crystal structure of sliding DNA clamp of Clostridioides difficile | | Descriptor: | Beta sliding clamp, TRIETHYLENE GLYCOL | | Authors: | Hishiki, A, Okazaki, S, Hara, K, Hashimoto, H. | | Deposit date: | 2022-06-29 | | Release date: | 2022-10-19 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.13 Å) | | Cite: | Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile.
J.Biochem., 173, 2022
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7Y9Y
 | | Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex | | Descriptor: | CHAT domain-containing protein, CRISPR-associated RAMP family protein, RNA (27-MER), ... | | Authors: | Kato, K, Okazaki, S, Ishikawa, J, Isayama, Y, Nishizawa, T, Nishimasu, H. | | Deposit date: | 2022-06-26 | | Release date: | 2022-11-09 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (2.77 Å) | | Cite: | RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease.
Science, 378, 2022
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7Y9X
 | | Structure of the Cas7-11-Csx29-guide RNA complex | | Descriptor: | CHAT domain-containing protein, CRISPR-associated RAMP family protein, ZINC ION, ... | | Authors: | Kato, K, Okazaki, S, Ishikawa, J, Isayama, Y, Nishizawa, T, Nishimasu, H. | | Deposit date: | 2022-06-26 | | Release date: | 2022-11-09 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (2.49 Å) | | Cite: | RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease.
Science, 378, 2022
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6KBC
 | | Crystal structure of CghA with Sch210972 | | Descriptor: | (2S)-3-[(2S,4E)-4-[[(1R,2S,4aR,6S,8R,8aS)-2-[(E)-but-2-en-2-yl]-6,8-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-oxidanyl-methylidene]-3,5-bis(oxidanylidene)pyrrolidin-2-yl]-2-methyl-2-oxidanyl-propanoic acid, CghA | | Authors: | Hara, K, Hashimoto, H, Maeda, N, Sato, M, Watanabe, K. | | Deposit date: | 2019-06-24 | | Release date: | 2020-06-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Catalytic mechanism and endo-to-exo selectivity reversion of an octalin-forming natural Diels-Alderase
Nat Catal, 2021
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6KJG
 | | Crystal structure of PsoF | | Descriptor: | Dual-functional monooxygenase/methyltransferase psoF | | Authors: | Hara, K, Hashimoto, H, Matsushita, T, Tsunematsu, Y, Watanabe, K. | | Deposit date: | 2019-07-22 | | Release date: | 2019-09-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Functional and Structural Analyses oftrans C-Methyltransferase in Fungal Polyketide Biosynthesis.
Biochemistry, 58, 2019
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6KJI
 | | Crystal structure of PsoF with SAH | | Descriptor: | Dual-functional monooxygenase/methyltransferase psoF, S-ADENOSYL-L-HOMOCYSTEINE, SULFATE ION | | Authors: | Hara, K, Hashimoto, H, Matsushita, T, Tsunematsu, Y, Watanabe, K. | | Deposit date: | 2019-07-22 | | Release date: | 2019-09-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Functional and Structural Analyses oftrans C-Methyltransferase in Fungal Polyketide Biosynthesis.
Biochemistry, 58, 2019
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8YHR
 | | DHODH in complex with furocoumavirin | | Descriptor: | 4-methyl-8-[(S)-oxidanyl(phenyl)methyl]-9-phenyl-furo[2,3-h]chromen-2-one, ACETATE ION, Dihydroorotate dehydrogenase (quinone), ... | | Authors: | Hara, K, Okumura, H, Nakahara, M, Sato, M, Hashimoto, H, Osada, H, Watanabe, K. | | Deposit date: | 2024-02-28 | | Release date: | 2024-05-22 | | Last modified: | 2024-06-05 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural and Functional Analyses of Inhibition of Human Dihydroorotate Dehydrogenase by Antiviral Furocoumavirin.
Biochemistry, 63, 2024
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2DCT
 | | Crystal structure of the TT1209 from Thermus thermophilus HB8 | | Descriptor: | CHLORIDE ION, SODIUM ION, hypothetical protein TTHA0104 | | Authors: | Asada, Y, Sugahara, M, Shimizu, K, Yamamoto, H, Shimada, H, Nakamoto, T, Ono, N, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-01-12 | | Release date: | 2006-01-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Crystal structure of the TT1209 from Thermus thermophilus HB8
To be Published
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1PKF
 | | Crystal Structure of Epothilone D-bound Cytochrome P450epoK | | Descriptor: | EPOTHILONE D, PROTOPORPHYRIN IX CONTAINING FE, cytochrome p450EpoK | | Authors: | Nagano, S, Li, H, Shimizu, H, Nishida, C, Ogura, H, Ortiz de Montellano, P.R, Poulos, T.L. | | Deposit date: | 2003-06-05 | | Release date: | 2003-10-28 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of Epothilone D-bound, Epothilone B-bound, and Substrate-free Forms of Cytochrome P450epoK
J.Biol.Chem., 278, 2003
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1Q5D
 | | Epothilone B-bound Cytochrome P450epoK | | Descriptor: | 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE, P450 epoxidase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagano, S, Li, H, Shimizu, H, Nishida, C, Ogura, H, Ortiz de Montellano, P.R, Poulos, T.L. | | Deposit date: | 2003-08-06 | | Release date: | 2003-10-28 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Crystal structures of epothilone D-bound, epothilone B-bound, and substrate-free forms of cytochrome P450epoK
J.Biol.Chem., 278, 2003
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1Q5E
 | | Substrate-free Cytochrome P450epoK | | Descriptor: | P450 epoxidase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagano, S, Li, H, Shimizu, H, Nishida, C, Ogura, H, Ortiz de Montellano, P.R, Poulos, T.L. | | Deposit date: | 2003-08-06 | | Release date: | 2003-10-28 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Crystal structures of epothilone D-bound, epothilone B-bound, and substrate-free forms of cytochrome P450epoK
J.Biol.Chem., 278, 2003
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4PDT
 | | Japanese Marasmius oreades lectin | | Descriptor: | Mannose recognizing lectin, SULFATE ION | | Authors: | Noma, Y, Shimokawa, M, Maeganeku, C, Motoshima, H, Watanabe, K, Minami, Y, Yagi, F. | | Deposit date: | 2014-04-22 | | Release date: | 2015-04-29 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | The structure of Japanese Marasmius oreades lectin at 1.40 Angstroms resolution.
To Be Published
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3B1U
 | | Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine | | Descriptor: | 2-{[(2S)-1-amino-5-{[(1Z)-2-fluoroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid, CALCIUM ION, Protein-arginine deiminase type-4, ... | | Authors: | Causey, C.P, Jones, J.E, Slack, J.L, Kamei, D, Jones Jr, L.E, Subramanian, V, Knuckley, B, Ebrahimi, P, Chumanevich, A.A, Luo, Y, Hashimoto, H, Shimizu, T, Sato, M, Hofseth, L.J, Thompson, P.R. | | Deposit date: | 2011-07-13 | | Release date: | 2011-10-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors
J.Med.Chem., 54, 2011
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3B1T
 | | Crystal structure of human peptidylarginine deiminase 4 in complex with o-Cl-amidine | | Descriptor: | 2-{[(2S)-1-amino-5-{[(1Z)-2-chloroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid, CALCIUM ION, Protein-arginine deiminase type-4, ... | | Authors: | Causey, C.P, Jones, J.E, Slack, J.L, Kamei, D, Jones Jr, L.E, Subramanian, V, Knuckley, B, Ebrahimi, P, Chumanevich, A.A, Luo, Y, Hashimoto, H, Shimizu, T, Sato, M, Hofseth, L.J, Thompson, P.R. | | Deposit date: | 2011-07-13 | | Release date: | 2011-10-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors
J.Med.Chem., 54, 2011
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4TKC
 | | Japanese Marasmius oreades lectin complexed with mannose | | Descriptor: | GLYCEROL, Mannose recognizing lectin, alpha-D-mannopyranose, ... | | Authors: | Noma, Y, Shimokawa, M, Maeganeku, C, Motoshima, H, Watanabe, K, Minami, Y, Yagi, F. | | Deposit date: | 2014-05-26 | | Release date: | 2015-06-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.29 Å) | | Cite: | Structure of Japanese Marasmius oreades lectin complexed with mannose.
To Be Published
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1UHN
 | | The crystal structure of the calcium binding protein AtCBL2 from Arabidopsis thaliana | | Descriptor: | CALCIUM ION, calcineurin B-like protein 2 | | Authors: | Nagae, M, Nozawa, A, Koizumi, N, Sano, H, Hashimoto, H, Sato, M, Shimizu, T. | | Deposit date: | 2003-07-07 | | Release date: | 2003-11-04 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The Crystal Structure of the Novel Calcium-binding Protein AtCBL2 from Arabidopsis thaliana
J.Biol.Chem., 278, 2003
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2RU7
 | | Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein | | Descriptor: | P16 peptide from Major prion protein, RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') | | Authors: | Hayashi, T, Oshima, H, Mashima, T, Nagata, T, Katahira, M, Kinoshita, M. | | Deposit date: | 2013-12-24 | | Release date: | 2014-05-21 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.
Nucleic Acids Res., 42, 2014
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5FHI
 | | Crystallographic structure of PsoE without Co | | Descriptor: | GLUTATHIONE, Glutathione S-transferase, putative | | Authors: | Hara, K, Hashimoto, H, Yamamoto, T, Tsunematsu, Y, Watanabe, K. | | Deposit date: | 2015-12-22 | | Release date: | 2016-04-20 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.41 Å) | | Cite: | Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis.
Angew. Chem. Int. Ed. Engl., 55, 2016
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5F8B
 | | Crystallographic Structure of PsoE with Co | | Descriptor: | (5~{S},8~{S},9~{R})-2-[(~{E})-hex-1-enyl]-8-methoxy-3-methyl-9-oxidanyl-8-(phenylcarbonyl)-1-oxa-7-azaspiro[4.4]non-2-ene-4,6-dione, COBALT (II) ION, GLUTATHIONE, ... | | Authors: | Hara, K, Hashimoto, H, Yamamoto, T, Tsunematsu, Y, Watanabe, K. | | Deposit date: | 2015-12-09 | | Release date: | 2016-04-20 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.54 Å) | | Cite: | Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis.
Angew. Chem. Int. Ed. Engl., 55, 2016
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