6FDC
 
 | | Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a | | Descriptor: | (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol, (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol, 1,2-ETHANEDIOL, ... | | Authors: | Prosdocimi, T, Donini, S, Parisini, E. | | Deposit date: | 2017-12-22 | | Release date: | 2018-05-16 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.
Biochemistry, 57, 2018
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7CQJ
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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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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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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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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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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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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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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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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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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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1J8K
 | | NMR STRUCTURE OF THE FIBRONECTIN EDA DOMAIN, NMR, 20 STRUCTURES | | Descriptor: | FIBRONECTIN | | Authors: | Niimi, T, Osawa, M, Yamaji, N, Yasunaga, K, Sakashita, H, Mase, T, Tanaka, A, Fujita, S. | | Deposit date: | 2001-05-22 | | Release date: | 2002-02-06 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | NMR structure of human fibronectin EDA.
J.Biomol.NMR, 21, 2001
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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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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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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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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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1A0B
 | | HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERICHIA COLI | | Descriptor: | AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB, ZINC ION | | Authors: | Kato, M, Mizuno, T, Shimizu, T, Hakoshima, T. | | Deposit date: | 1997-11-27 | | Release date: | 1998-03-18 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Insights into multistep phosphorelay from the crystal structure of the C-terminal HPt domain of ArcB.
Cell(Cambridge,Mass.), 88, 1997
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8ISN
 | | HLA-A24 in complex with modified 9mer WT1 peptide | | Descriptor: | Beta-2-microglobulin, CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU, GLYCEROL, ... | | Authors: | Bekker, G.J, Numoto, N, Kawasaki, M, Hayashi, T, Yabuno, S, Kozono, Y, Shimizu, T, Kozono, H, Ito, N, Oda, M, Kamiya, N. | | Deposit date: | 2023-03-21 | | Release date: | 2023-09-13 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.48 Å) | | Cite: | Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.
Protein Sci., 32, 2023
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7DHW
 | | Crystal structure of myosin-XI motor domain in complex with ADP-ALF4 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Suzuki, K, Haraguchi, T, Tamanaha, M, Yoshimura, K, Imi, T, Tominaga, M, Sakayama, H, Nishiyama, T, Ito, K, Murata, T. | | Deposit date: | 2020-11-17 | | Release date: | 2021-05-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.84 Å) | | Cite: | Discovery of ultrafast myosin, its amino acid sequence, and structural features.
Proc.Natl.Acad.Sci.USA, 119, 2022
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6IU0
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7BY1
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4R07
 | | Crystal structure of human TLR8 in complex with ORN06 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate), ... | | Authors: | Tanji, H, Ohto, U, Shibata, T, Taoka, M, Yamauchi, Y, Isobe, T, Miyake, K, Shimizu, T. | | Deposit date: | 2014-07-30 | | Release date: | 2015-01-14 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Toll-like receptor 8 senses degradation products of single-stranded RNA
Nat.Struct.Mol.Biol., 22, 2015
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4R09
 | | Crystal structure of human TLR8 in complex with ORN06S | | Descriptor: | 1-[(2R,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Tanji, H, Ohto, U, Shimizu, T. | | Deposit date: | 2014-07-30 | | Release date: | 2015-01-14 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.62 Å) | | Cite: | Toll-like receptor 8 senses degradation products of single-stranded RNA.
Nat.Struct.Mol.Biol., 22, 2015
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7BPR
 | | Crystal structure of human TEX101 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, PLATINUM (II) ION, Testis-expressed protein 101 | | Authors: | Masutani, M, Sakurai, S, Shimizu, T, Ohto, U. | | Deposit date: | 2020-03-23 | | Release date: | 2020-07-15 | | Last modified: | 2020-12-23 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Crystal structure of TEX101, a glycoprotein essential for male fertility, reveals the presence of tandemly arranged Ly6/uPAR domains.
Febs Lett., 594, 2020
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