1A0A
| PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX | Descriptor: | DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3'), DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3'), PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4) | Authors: | Shimizu, T, Toumoto, A, Ihara, K, Shimizu, M, Kyogoku, Y, Ogawa, N, Oshima, Y, Hakoshima, T. | Deposit date: | 1997-11-27 | Release date: | 1998-03-18 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J., 16, 1997
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7YTX
| Crystal structure of TLR8 in complex with its antagonist | Descriptor: | (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Shimizu, T, Sakaniwa, K. | Deposit date: | 2022-08-16 | Release date: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | A novel Toll-like receptor 7/8-specific antagonist E6742 ameliorates clinically relevant disease parameters in murine models of lupus. Eur.J.Pharmacol., 957, 2023
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1KCD
| Endopolygalacturonase I from Stereum purpureum complexed with two galacturonate at 1.15 A resolution. | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ENDOPOLYGALACTURONASE, ... | Authors: | Shimizu, T, Nakatsu, T, Miyairi, K, Okuno, T, Kato, H. | Deposit date: | 2001-11-08 | Release date: | 2002-06-05 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.15 Å) | Cite: | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry, 41, 2002
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1KCC
| Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution. | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ENDOPOLYGALACTURONASE, ... | Authors: | Shimizu, T, Nakatsu, T, Miyairi, K, Okuno, T, Kato, H. | Deposit date: | 2001-11-08 | Release date: | 2002-06-05 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1 Å) | Cite: | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry, 41, 2002
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1K5C
| Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ENDOPOLYGALACTURONASE, ... | Authors: | Shimizu, T, Nakatsu, T, Miyairi, K, Okuno, T, Kato, H. | Deposit date: | 2001-10-10 | Release date: | 2002-06-05 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (0.96 Å) | Cite: | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry, 41, 2002
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5HN4
| Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate | Descriptor: | (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid, Homoisocitrate dehydrogenase, IMIDAZOLE, ... | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | Deposit date: | 2016-01-18 | Release date: | 2016-12-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.64 Å) | Cite: | Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis Biochem. J., 474, 2017
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5HN6
| Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and 3-isopropylmalate | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 3-ISOPROPYLMALIC ACID, Homoisocitrate dehydrogenase, ... | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | Deposit date: | 2016-01-18 | Release date: | 2016-12-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis Biochem. J., 474, 2017
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5HN5
| Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and isocitrate | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Homoisocitrate dehydrogenase, ISOCITRIC ACID, ... | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | Deposit date: | 2016-01-18 | Release date: | 2016-12-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis Biochem. J., 474, 2017
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5HN3
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5EIN
| Crystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+ and LysW-gamma-aminoadipic acid | Descriptor: | Alpha-aminoadipate carrier protein LysW, FORMIC ACID, N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase, ... | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | Deposit date: | 2015-10-30 | Release date: | 2016-03-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal Structure of the LysYLysW Complex from Thermus thermophilus. J.Biol.Chem., 291, 2016
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5EIO
| Crystal structure of LysY from Thermus thermophilus complexed with NADP+ and LysW-gamma-aminoadipic semialdehyde | Descriptor: | ACETIC ACID, N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | Deposit date: | 2015-10-30 | Release date: | 2016-03-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal Structure of the LysYLysW Complex from Thermus thermophilus. J.Biol.Chem., 291, 2016
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5GIC
| Crystal structure of VDR in complex with DLAM-2P | Descriptor: | (3~{R},5~{S})-5-[(2~{R})-2-[(1~{R},3~{a}~{S},4~{Z},7~{a}~{R})-7~{a}-methyl-4-[(2~{E})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(2-phenylethyl)pyrrolidin-2-one, SRC1, Vitamin D3 receptor | Authors: | Shimizu, T, Asano, L. | Deposit date: | 2016-06-23 | Release date: | 2016-12-07 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.352 Å) | Cite: | Regulation of the vitamin D receptor by vitamin D lactam derivatives. Febs Lett., 590, 2016
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1ISN
| Crystal structure of merlin FERM domain | Descriptor: | merlin | Authors: | Shimizu, T, Seto, A, Maita, N, Hamada, K, Tsukita, S, Tsukita, S, Hakoshima, T. | Deposit date: | 2001-12-13 | Release date: | 2002-04-03 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structural basis for neurofibromatosis type 2. Crystal structure of the merlin FERM domain. J.Biol.Chem., 277, 2002
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1DPF
| CRYSTAL STRUCTURE OF A MG-FREE FORM OF RHOA COMPLEXED WITH GDP | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, RHOA | Authors: | Shimizu, T, Ihara, K, Maesaki, R, Kuroda, S, Kaibuchi, K, Hakoshima, T. | Deposit date: | 1999-12-27 | Release date: | 2000-06-21 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | An open conformation of switch I revealed by the crystal structure of a Mg2+-free form of RHOA complexed with GDP. Implications for the GDP/GTP exchange mechanism. J.Biol.Chem., 275, 2000
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1VMO
| CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VMO-I): A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY STRUCTURES RELATED BY AN INTERNAL THREE-FOLD SYMMETRY | Descriptor: | VITELLINE MEMBRANE OUTER LAYER PROTEIN I | Authors: | Shimizu, T, Vassylyev, D.G, Kido, S, Doi, Y, Morikawa, K. | Deposit date: | 1994-01-06 | Release date: | 1994-05-31 | Last modified: | 2024-06-05 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry. EMBO J., 13, 1994
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1UIX
| Coiled-coil structure of the RhoA-binding domain in Rho-kinase | Descriptor: | Rho-associated kinase | Authors: | Shimizu, T, Ihara, K, Maesaki, R, Amano, M, Kaibuchi, K, Hakoshima, T. | Deposit date: | 2003-07-23 | Release date: | 2003-10-21 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Parallel coiled-coil association of the RhoA-binding domain in Rho-kinase J.Biol.Chem., 278, 2003
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3W0I
| Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands | Descriptor: | (2S)-3-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)pentan-3-yl]phenoxy}propane-1,2-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 Receptor | Authors: | Shimizu, T, Asano, L, Kuwabara, N, Ito, I, Waku, T, Yanagisawa, J, Miyachi, H. | Deposit date: | 2012-10-30 | Release date: | 2013-10-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands. Febs Lett., 587, 2013
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3W0H
| Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands | Descriptor: | (2S)-3-{4-[4-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)heptan-4-yl]phenoxy}propane-1,2-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Shimizu, T, Asano, L, Kuwabara, N, Ito, I, Waku, T, Yanagisawa, J, Miyachi, H. | Deposit date: | 2012-10-30 | Release date: | 2013-10-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands. Febs Lett., 587, 2013
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3W0G
| Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands | Descriptor: | (2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)propan-2-yl]phenoxy}propane-1,2-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Shimizu, T, Asano, L, Kuwabara, N, Ito, I, Waku, T, Yanagisawa, J, Miyachi, H. | Deposit date: | 2012-10-30 | Release date: | 2013-10-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands. Febs Lett., 587, 2013
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3W0J
| Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands | Descriptor: | (2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propan-2-yl]-2-methylphenoxy}propane-1,2-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 Receptor | Authors: | Shimizu, T, Asano, L, Kuwabara, N, Ito, I, Waku, T, Yanagisawa, J, Miyachi, H. | Deposit date: | 2012-10-30 | Release date: | 2013-10-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands. Febs Lett., 587, 2013
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4UB8
| Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | Deposit date: | 2014-08-12 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature, 517, 2015
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4UB6
| Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | Deposit date: | 2014-08-12 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature, 517, 2015
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7CRF
| Crystal structure of human TLR8 in complex with CU-CPD107 | Descriptor: | 1-[2-(ethoxymethyl)-4-iodanyl-5-phenyl-imidazol-1-yl]-2-methyl-propan-2-ol, 2-acetamido-2-deoxy-beta-D-glucopyranose, Toll-like receptor 8, ... | Authors: | Sakaniwa, K, Tanji, H, Ohto, U, Shimizu, T. | Deposit date: | 2020-08-13 | Release date: | 2021-06-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.89 Å) | Cite: | Tetrasubstituted imidazoles as incognito Toll-like receptor 8 a(nta)gonists. Nat Commun, 12, 2021
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7C77
| Cryo-EM structure of mouse TLR3 in complex with UNC93B1 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Protein unc-93 homolog B1, ... | Authors: | Ohto, U, Ishida, H, Shimizu, T. | Deposit date: | 2020-05-23 | Release date: | 2021-01-06 | Last modified: | 2021-02-24 | Method: | ELECTRON MICROSCOPY (3.3 Å) | Cite: | Cryo-EM structures of Toll-like receptors in complex with UNC93B1. Nat.Struct.Mol.Biol., 28, 2021
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7C76
| Cryo-EM structure of human TLR3 in complex with UNC93B1 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Protein unc-93 homolog B1, ... | Authors: | Ohto, U, Ishida, H, Shimizu, T. | Deposit date: | 2020-05-23 | Release date: | 2021-01-06 | Last modified: | 2021-02-24 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Cryo-EM structures of Toll-like receptors in complex with UNC93B1. Nat.Struct.Mol.Biol., 28, 2021
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