1VMO
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![BU of 1vmo by Molmil](/molmil-images/mine/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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5HN4
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![BU of 5hn4 by Molmil](/molmil-images/mine/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
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![BU of 5hn6 by Molmil](/molmil-images/mine/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
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![BU of 5hn5 by Molmil](/molmil-images/mine/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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1A0A
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![BU of 1a0a by Molmil](/molmil-images/mine/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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1KCD
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![BU of 1kcd by Molmil](/molmil-images/mine/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
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![BU of 1kcc by Molmil](/molmil-images/mine/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
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![BU of 1k5c by Molmil](/molmil-images/mine/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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1DPF
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![BU of 1dpf by Molmil](/molmil-images/mine/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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5EIO
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![BU of 5eio by Molmil](/molmil-images/mine/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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5EIN
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![BU of 5ein by Molmil](/molmil-images/mine/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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1ISN
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![BU of 1isn by Molmil](/molmil-images/mine/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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1UIX
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![BU of 1uix by Molmil](/molmil-images/mine/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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7YTX
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![BU of 7ytx by Molmil](/molmil-images/mine/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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3W0I
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![BU of 3w0i by Molmil](/molmil-images/mine/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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5GIC
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![BU of 5gic by Molmil](/molmil-images/mine/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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3W0H
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![BU of 3w0h by Molmil](/molmil-images/mine/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
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![BU of 3w0g by Molmil](/molmil-images/mine/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
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![BU of 3w0j by Molmil](/molmil-images/mine/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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3B0T
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![BU of 3b0t by Molmil](/molmil-images/mine/3b0t) | Human VDR ligand binding domain in complex with maxacalcitol | Descriptor: | (1S,3R,5Z,7E,14beta,17alpha,20S)-20-(3-hydroxy-3-methylbutoxy)-9,10-secopregna-5,7,10-triene-1,3-diol, SULFATE ION, Vitamin D3 receptor | Authors: | Hishiki, A, Hashimoto, H, Sato, M, Shimizu, T. | Deposit date: | 2011-06-14 | Release date: | 2011-08-10 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | Human VDR ligand binding domain in complex with maxacalcitol To be Published
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3B0R
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![BU of 3b0r by Molmil](/molmil-images/mine/3b0r) | |
4UB6
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![BU of 4ub6 by Molmil](/molmil-images/mine/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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7YTP
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![BU of 7ytp by Molmil](/molmil-images/mine/7ytp) | TLR7 in complex with an inhibitor | 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: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2022-08-15 | Release date: | 2023-11-15 | Method: | ELECTRON MICROSCOPY (2.77 Å) | Cite: | TLR7 in complex with an inhibitor To Be Published
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5IRN
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![BU of 5irn by Molmil](/molmil-images/mine/5irn) | |