2YVF
| Crystal structure of ferredoxin reductase BPHA4 (hydroquinone) | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, FORMIC ACID, Ferredoxin reductase, ... | Authors: | Senda, T, Senda, M. | Deposit date: | 2007-04-12 | Release date: | 2007-10-16 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin J.Mol.Biol., 373, 2007
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7E18
| Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53 | Descriptor: | 1,2-ETHANEDIOL, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1ab | Authors: | Senda, M, Konno, S, Hayashi, Y, Senda, T. | Deposit date: | 2021-02-01 | Release date: | 2021-06-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents. J.Med.Chem., 65, 2022
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7E19
| Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5 | Descriptor: | (phenylmethyl) N-[(2S)-1-[[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate, 3C-like proteinase | Authors: | Senda, M, Konno, S, Hayashi, Y, Senda, T. | Deposit date: | 2021-02-01 | Release date: | 2021-06-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents. J.Med.Chem., 65, 2022
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7C5W
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7C5X
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7C5V
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7C5Y
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7EM6
| Crystal structure of the PI5P4Kbeta N203D-ITP complex | Descriptor: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM2
| Crystal structure of the PI5P4Kbeta-XTP complex | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM1
| Crystal structure of the PI5P4Kbeta-ITP complex | Descriptor: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM7
| Crystal structure of the PI5P4Kbeta N203D-XTP complex | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.45 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM5
| Crystal structure of the PI5P4Kbeta F205L-XTP complex | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM4
| Crystal structure of the PI5P4Kbeta F205L-ITP complex | Descriptor: | INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM3
| Crystal structure of the PI5P4Kbeta-2a-ATP complex | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7EM8
| Crystal structure of the PI5P4Kbeta T201M-2a-ATP complex | Descriptor: | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | Authors: | Senda, M, Senda, T. | Deposit date: | 2021-04-13 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.05 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 30, 2022
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7DNN
| Crystal structure of the AgCarB2-C2 complex with homoorientin | Descriptor: | 2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one, AP_endonuc_2 domain-containing protein, AgCarC2, ... | Authors: | Senda, M, Kumano, T, Watanabe, S, Kobayashi, M, Senda, T. | Deposit date: | 2020-12-10 | Release date: | 2021-10-20 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria Nat Commun, 2021
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7DNM
| Crystal structure of the AgCarB2-C2 complex | Descriptor: | AP_endonuc_2 domain-containing protein, AgCarC2, IODIDE ION, ... | Authors: | Senda, M, Kumano, T, Watanabe, S, Kobayashi, M, Senda, T. | Deposit date: | 2020-12-10 | Release date: | 2021-10-20 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria Nat Commun, 2021
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7DVE
| Crystal structure of FAD-dependent C-glycoside oxidase | Descriptor: | 6'''-hydroxyparomomycin C oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION | Authors: | Senda, M, Watanabe, S, Kumano, T, Kobayashi, M, Senda, T. | Deposit date: | 2021-01-13 | Release date: | 2021-09-08 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | FAD-dependent C -glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis. Proc.Natl.Acad.Sci.USA, 118, 2021
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7D98
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4DVY
| Crystal structure of the Helicobacter pylori CagA oncoprotein | Descriptor: | Cytotoxicity-associated immunodominant antigen | Authors: | Hayashi, T, Senda, M, Morohashi, H, Higashi, H, Horio, M, Kashiba, Y, Nagase, L, Sasaya, D, Shimizu, T, Venugopalan, N, Kumeta, H, Noda, N, Inagaki, F, Senda, T, Hatakeyama, M. | Deposit date: | 2012-02-23 | Release date: | 2012-07-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Tertiary Structure-Function Analysis Reveals the Pathogenic Signaling Potentiation Mechanism of Helicobacter pylori Oncogenic Effector CagA Cell Host Microbe, 12, 2012
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4DVZ
| Crystal structure of the Helicobacter pylori CagA oncoprotein | Descriptor: | Cytotoxicity-associated immunodominant antigen | Authors: | Hayashi, T, Senda, M, Morohashi, H, Higashi, H, Horio, M, Kashiba, Y, Nagase, L, Sasaya, D, Shimizu, T, Venugopalan, N, Kumeta, H, Noda, N, Inagaki, F, Senda, T, Hatakeyama, M. | Deposit date: | 2012-02-23 | Release date: | 2012-07-25 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3.19 Å) | Cite: | Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA Cell Host Microbe, 12, 2012
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2E50
| Crystal structure of SET/TAF-1beta/INHAT | Descriptor: | Protein SET, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose | Authors: | Muto, S, Senda, M, Senda, T, Horikoshi, M. | Deposit date: | 2006-12-18 | Release date: | 2007-02-20 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity Proc.Natl.Acad.Sci.Usa, 104, 2007
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6K4H
| Crystal structure of the PI5P4Kbeta-AMPPNP complex | Descriptor: | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | Authors: | Takeuchi, K, Senda, M, Senda, T. | Deposit date: | 2019-05-23 | Release date: | 2020-05-27 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 2022
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6K4G
| Crystal structure of the PI5P4Kbeta-GMPPNP complex | Descriptor: | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | Authors: | Takeuchi, K, Senda, M, Senda, T. | Deposit date: | 2019-05-23 | Release date: | 2020-05-27 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Structure, 2022
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8JW3
| The crystal structure of the viral terpene synthase from Orpheovirus IHUMI-LCC2 | Descriptor: | SULFATE ION, Terpenoid synthase | Authors: | Jung, Y, Mitsuhashi, T, Senda, M, Sato, S, Senda, T, Fujita, M. | Deposit date: | 2023-06-28 | Release date: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome. J.Am.Chem.Soc., 145, 2023
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