1V9H
 
 | | Crystal structure of the RNase MC1 mutant Y101A in complex with 5'-UMP | | Descriptor: | Ribonuclease MC, SULFATE ION, URIDINE-5'-MONOPHOSPHATE | | Authors: | Kimura, K, Numata, T, Kakuta, Y, Kimura, M. | | Deposit date: | 2004-01-26 | | Release date: | 2004-10-05 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Amino acids conserved at the C-terminal half of the ribonuclease t2 family contribute to protein stability of the enzymes
Biosci.Biotechnol.Biochem., 68, 2004
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1VE8
 | | X-Ray analyses of oligonucleotides containing 5-formylcytosine, suggesting a structural reason for codon-anticodon recognition of mitochondrial tRNA-Met; Part 1, d(CGCGAATT(f5C)GCG) | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5FC)P*GP*CP*G)-3', SODIUM ION | | Authors: | Kimura, K, Ono, A, Watanabe, K, Takenaka, A. | | Deposit date: | 2004-03-29 | | Release date: | 2005-06-28 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | X-Ray analyses of oligonucleotides containing 5-formylcytosine, suggest a structural reason for the codon-anticodon recognition of mitochondrial tRNA-Met
To be Published
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7ECD
 | | Crystal structure of Tam41 from Firmicutes bacterium, complex with CTP-Mg | | Descriptor: | BROMIDE ION, CYTIDINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Kimura, K, Kawai, F, Kubota-Kawai, H, Watanabe, Y, Tamura, Y. | | Deposit date: | 2021-03-12 | | Release date: | 2022-01-19 | | Last modified: | 2022-04-13 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure of Tam41 cytidine diphosphate diacylglycerol synthase from a Firmicutes bacterium.
J.Biochem., 171, 2022
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6SHL
 | | Structure of a marine algae virus of the order Picornavirales | | Descriptor: | VP1, VP2, VP3, ... | | Authors: | Munke, A, Tomaru, Y, Kimura, K, Okamoto, K. | | Deposit date: | 2019-08-07 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Capsid Structure of a Marine Algal Virus of the Order Picornavirales .
J.Virol., 94, 2020
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1X0T
 | | Crystal structure of ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3 | | Descriptor: | Ribonuclease P protein component 4, ZINC ION | | Authors: | Kakuta, Y, Ishimatsu, I, Numata, T, Kimura, K, Yao, M, Tanaka, I, Kimura, M. | | Deposit date: | 2005-03-29 | | Release date: | 2005-11-15 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal Structure of a Ribonuclease P Protein Ph1601p from Pyrococcus horikoshii OT3: An Archaeal Homologue of Human Nuclear Ribonuclease P Protein Rpp21(,)
Biochemistry, 44, 2005
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1J1G
 | | Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP | | Descriptor: | GUANOSINE-5'-MONOPHOSPHATE, Ribonuclease MC1 | | Authors: | Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M. | | Deposit date: | 2002-12-04 | | Release date: | 2003-05-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity
Biochemistry, 42, 2003
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1J1F
 | | Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP | | Descriptor: | GUANOSINE-5'-MONOPHOSPHATE, RIBONUCLEASE MC1 | | Authors: | Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M. | | Deposit date: | 2002-12-03 | | Release date: | 2003-05-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity
Biochemistry, 42, 2003
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3WNP
 | | D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoundecaose | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CALCIUM ION, Cycloisomaltooligosaccharide glucanotransferase, ... | | Authors: | Suzuki, R, Suzuki, N, Fujimoto, Z, Momma, M, Kimura, K, Kitamura, S, Kimura, A, Funane, K. | | Deposit date: | 2013-12-10 | | Release date: | 2014-02-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Molecular engineering of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040: structural determinants for the reaction product size and reactivity.
Biochem.J., 467, 2015
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2D57
 | | Double layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3.2 a resolution by electron crystallography | | Descriptor: | Aquaporin-4 | | Authors: | Hiroaki, Y, Tani, K, Kamegawa, A, Gyobu, N, Nishikawa, K, Suzuki, H, Walz, T, Sasaki, S, Mitsuoka, K, Kimura, K, Mizoguchi, A, Fujiyoshi, Y. | | Deposit date: | 2005-10-29 | | Release date: | 2006-01-31 | | Last modified: | 2023-11-08 | | Method: | ELECTRON CRYSTALLOGRAPHY (3.2 Å) | | Cite: | Implications of the Aquaporin-4 Structure on Array Formation and Cell Adhesion
J.Mol.Biol., 355, 2005
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1ID6
 | | SOLUTION STRUCTURES OF SYR6 | | Descriptor: | SYR6 | | Authors: | Sato, A, Kawaguchi, K, Kimura, K, Tanimura, R, Sone, S. | | Deposit date: | 2001-04-04 | | Release date: | 2002-04-10 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | A peptide mimetic of IFN, the first proof of a small peptidic agonist for heterodimeric cytokine receptor
To be Published
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1ID7
 | | SOLUTION STRUCTURE OF SYR6 | | Descriptor: | SYR6 | | Authors: | Sato, A, Kawaguchi, K, Kimura, K, Tanimura, R, Sone, S. | | Deposit date: | 2001-04-04 | | Release date: | 2002-04-10 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | A peptide mimetic of IFN, the first proof of a small peptidic agonist for heterodimeric cytokine receptor
To be Published
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3A9L
 | | Structure of Bacteriophage poly-gamma-glutamate hydrolase | | Descriptor: | PHOSPHATE ION, Poly-gamma-glutamate hydrolase, ZINC ION | | Authors: | Fujimoto, Z, Kimura, K. | | Deposit date: | 2009-10-30 | | Release date: | 2010-11-10 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of bacteriophage PhiNIT1 zinc peptidase PghP that hydrolyzes gamma-glutamyl linkage of bacterial poly-gamma-glutamate
Proteins, 80, 2012
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7CD3
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7CD4
 | | Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein. | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, MAGNESIUM ION, ... | | Authors: | Fujimoto, Z, Kishine, N, Kimura, K. | | Deposit date: | 2020-06-18 | | Release date: | 2021-03-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family.
Biosci.Biotechnol.Biochem., 85, 2021
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7CD2
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5Y6U
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8IF2
 | | Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ... | | Authors: | Kimura, K, Suzuki, T, Hashiguchi, T. | | Deposit date: | 2023-02-17 | | Release date: | 2023-05-17 | | Last modified: | 2023-05-24 | | Method: | X-RAY DIFFRACTION (2.78 Å) | | Cite: | Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Nat Commun, 14, 2023
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3FX5
 | | Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High Resolution X-ray Crystallography | | Descriptor: | (4R)-N-tert-butyl-3-[(2S,3S)-2-hydroxy-3-({N-[(isoquinolin-5-yloxy)acetyl]-S-methyl-L-cysteinyl}amino)-4-phenylbutanoyl]-1,3-thiazolidine-4-carboxamide, GLYCEROL, protease | | Authors: | Adachi, M, Ohhara, T, Tamada, T, Okazaki, N, Kuroki, R. | | Deposit date: | 2009-01-20 | | Release date: | 2009-03-24 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (0.93 Å) | | Cite: | Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography.
Proc.Natl.Acad.Sci.USA, 2009
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7NS0
 | | Bacilladnavirus capsid structure | | Descriptor: | Capsid protein VP2 | | Authors: | Munke, A, Okamoto, K. | | Deposit date: | 2021-03-05 | | Release date: | 2022-07-20 | | Last modified: | 2022-09-14 | | Method: | ELECTRON MICROSCOPY (2.4 Å) | | Cite: | Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses.
Mbio, 13, 2022
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7YV1
 | | Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Isoform 2B of GTPase KRas, KA30L Fab H-chain, ... | | Authors: | Irie, M, Fukami, T.A, Matsuo, A, Saka, K, Nishimura, M, Saito, H, Torizawa, T, Tanada, M, Ohta, A. | | Deposit date: | 2022-08-18 | | Release date: | 2023-07-26 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.454 Å) | | Cite: | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets.
J.Am.Chem.Soc., 145, 2023
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7YUZ
 | | Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784 | | Descriptor: | AP8784, GUANOSINE-5'-DIPHOSPHATE, IODIDE ION, ... | | Authors: | Irie, M, Fukami, T.A, Tanada, M, Ohta, A, Torizawa, T. | | Deposit date: | 2022-08-18 | | Release date: | 2023-07-26 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.878 Å) | | Cite: | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets.
J.Am.Chem.Soc., 145, 2023
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5WS3
 | | Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA | | Descriptor: | N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, ... | | Authors: | Suno, R, Kimura, K, Nakane, T, Yamashita, K, Wang, J, Fujiwara, T, Yamanaka, Y, Im, D, Tsujimoto, H, Sasanuma, M, Horita, S, Hirokawa, T, Nango, E, Tono, K, Kameshima, T, Hatsui, T, Joti, Y, Yabashi, M, Shimamoto, K, Yamamoto, M, Rosenbaum, D.M, Iwata, S, Shimamura, T, Kobayashi, T. | | Deposit date: | 2016-12-05 | | Release date: | 2017-12-13 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.
Structure, 26, 2018
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7XWA
 | | Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ... | | Authors: | Suzuki, T, Kimura, K, Hashiguchi, T. | | Deposit date: | 2022-05-26 | | Release date: | 2022-09-28 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.36 Å) | | Cite: | Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5.
Cell, 185, 2022
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1GTW
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1GU4
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