1QNF
 
 | | STRUCTURE OF PHOTOLYASE | | Descriptor: | 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE, FLAVIN-ADENINE DINUCLEOTIDE, PHOTOLYASE | | Authors: | Miki, K, Kitadokoro, K. | | Deposit date: | 1997-07-04 | | Release date: | 1998-01-14 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of DNA photolyase from Anacystis nidulans
Nat.Struct.Biol., 4, 1997
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1CO6
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1CRY
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1IO3
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2YQJ
 | | Crystal Structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the reaction-completed form | | Descriptor: | GLYCEROL, MAGNESIUM ION, SULFATE ION, ... | | Authors: | Miki, K, Maruyama, D, Nishitani, Y, Nonaka, T, Kita, A. | | Deposit date: | 2007-03-30 | | Release date: | 2007-05-22 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism
J.Biol.Chem., 282, 2007
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2YQC
 | | Crystal Structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the apo-like form | | Descriptor: | GLYCEROL, MAGNESIUM ION, UDP-N-acetylglucosamine pyrophosphorylase | | Authors: | Miki, K, Maruyama, D, Nishitani, Y, Nonaka, T, Kita, A. | | Deposit date: | 2007-03-30 | | Release date: | 2007-05-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism
J.Biol.Chem., 282, 2007
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2YQH
 | | Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the substrate-binding form | | Descriptor: | 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Miki, K, Maruyama, D, Nishitani, Y, Nonaka, T, Kita, A. | | Deposit date: | 2007-03-30 | | Release date: | 2007-05-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism
J.Biol.Chem., 282, 2007
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2YQS
 | | Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the product-binding form | | Descriptor: | GLYCEROL, MAGNESIUM ION, SULFATE ION, ... | | Authors: | Miki, K, Maruyama, D, Nishitani, Y, Nonaka, T, Kita, A. | | Deposit date: | 2007-03-30 | | Release date: | 2007-05-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism
J.Biol.Chem., 282, 2007
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4V8K
 | | Crystal structure of the LH1-RC complex from Thermochromatium tepidum in P21 form | | Descriptor: | BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN A, CALCIUM ION, ... | | Authors: | Niwa, S, Takeda, K, Wang-Otomo, Z.-Y, Miki, K. | | Deposit date: | 2013-11-22 | | Release date: | 2014-07-09 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (3.006 Å) | | Cite: | Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 angstrom
Nature, 508, 2014
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3KDO
 | | Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-10-23 | | Release date: | 2010-10-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.36 Å) | | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
J.Biol.Chem., 285, 2010
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3KDN
 | | Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-10-23 | | Release date: | 2010-10-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
J.Biol.Chem., 285, 2010
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6LOP
 | | Crystal Structure of Class IB terpene synthase bound with geranylgeraniol | | Descriptor: | (2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-ol, Tetraprenyl-beta-curcumene synthase | | Authors: | Fujihashi, M, Inagi, H, Miki, K. | | Deposit date: | 2020-01-07 | | Release date: | 2020-11-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate.
Acs Chem.Biol., 15, 2020
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6LOO
 | | Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate | | Descriptor: | Tetraprenyl-beta-curcumene synthase, phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate, phosphono [(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate | | Authors: | Fujihashi, M, Inagi, H, Miki, K. | | Deposit date: | 2020-01-07 | | Release date: | 2020-11-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate.
Acs Chem.Biol., 15, 2020
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2B3R
 | | Crystal structure of the C2 domain of class II phosphatidylinositide 3-kinase C2 | | Descriptor: | Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing alpha polypeptide, SULFATE ION | | Authors: | Liu, L, Song, X, He, D, Komma, C, Kita, A, Verbasius, J.V, Bellamy, H, Miki, K, Czech, M.P, Zhou, G.W. | | Deposit date: | 2005-09-20 | | Release date: | 2005-12-13 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the C2 domain of class II phosphatidylinositide 3-kinase C2alpha.
J.Biol.Chem., 281, 2006
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7BXV
 | | 11A1 antibody-peptide complex | | Descriptor: | 1,2-ETHANEDIOL, Fab of the 11A1 antibody H chain, Fab of the 11A1 antibody L chain, ... | | Authors: | Irie, K, Irie, Y, Kita, A, Miki, K. | | Deposit date: | 2020-04-21 | | Release date: | 2021-04-21 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | APOE epsilon 4 allele advances the age-dependent decline of amyloid beta clearance in the human cortex.
Biorxiv, 2022
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7Y3J
 | | 24B3 antibody-peptide complex | | Descriptor: | 24B3 Heavy chain, 24B3 Light chain, ALA-LEU-VAL-PHE-PHE-ALA-PRO-ALA-VAL-GLY-SER | | Authors: | Irie, K, Irie, Y, Kita, A, Miki, K. | | Deposit date: | 2022-06-11 | | Release date: | 2022-08-17 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis of the 24B3 antibody against the toxic conformer of amyloid beta with a turn at positions 22 and 23.
Biochem.Biophys.Res.Commun., 621, 2022
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1QSW
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3HRX
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3FF5
 | | Crystal structure of the conserved N-terminal domain of the peroxisomal matrix-protein-import receptor, Pex14p | | Descriptor: | Peroxisomal biogenesis factor 14, decyl 2-trimethylazaniumylethyl phosphate | | Authors: | Su, J.-R, Takeda, K, Tamura, S, Fujiki, Y, Miki, K. | | Deposit date: | 2008-12-01 | | Release date: | 2008-12-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of the conserved N-terminal domain of the peroxisomal matrix protein import receptor, Pex14p
Proc.Natl.Acad.Sci.USA, 106, 2009
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5WQQ
 | | High resolution structure of high-potential iron-sulfur protein in the oxidized state | | Descriptor: | GLYCEROL, High-potential iron-sulfur protein, IRON/SULFUR CLUSTER, ... | | Authors: | Ohno, H, Takeda, K, Niwa, S, Tsujinaka, T, Hanazono, Y, Hirano, Y, Miki, K. | | Deposit date: | 2016-11-28 | | Release date: | 2017-06-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (0.8 Å) | | Cite: | Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 angstrom resolution
PLoS ONE, 12, 2017
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4XF6
 | | myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate) | | Descriptor: | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, 1,2-ETHANEDIOL, ADENOSINE-5'-DIPHOSPHATE, ... | | Authors: | Nagata, R, Fujihashi, M, Miki, K. | | Deposit date: | 2014-12-26 | | Release date: | 2015-06-03 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.08 Å) | | Cite: | Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation
Biochemistry, 54, 2015
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4XF7
 | | myo-inositol 3-kinase bound with its substrates (AMPPCP and myo-inositol) | | Descriptor: | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, Carbohydrate/pyrimidine kinase, PfkB family, ... | | Authors: | Nagata, R, Fujihashi, M, Miki, K. | | Deposit date: | 2014-12-26 | | Release date: | 2015-06-03 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation
Biochemistry, 54, 2015
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5WQR
 | | High resolution structure of high-potential iron-sulfur protein in the reduced state | | Descriptor: | GLYCEROL, High-potential iron-sulfur protein, IRON/SULFUR CLUSTER, ... | | Authors: | Ohno, H, Takeda, K, Niwa, S, Tsujinaka, T, Hanazono, Y, Hirano, Y, Miki, K. | | Deposit date: | 2016-11-28 | | Release date: | 2017-06-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (0.8 Å) | | Cite: | Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 angstrom resolution
PLoS ONE, 12, 2017
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8H8Q
 | | Fab-amyloid beta fragment complex at neutral pH | | Descriptor: | CHLORIDE ION, Fab, GLN-LYS-CYS-VAL-PHE-PHE-ALA-GLU-ASP-VAL-GLY-SER-ASN-CYS-GLY, ... | | Authors: | Kita, A, Irie, K, Irie, Y, Matsushima, Y, Miki, K. | | Deposit date: | 2022-10-24 | | Release date: | 2023-10-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Fab-amyloid beta fragment complex at neutral pH
To Be Published
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8JVC
 | | Crystal structure of dephospho-coenzyme A kinase | | Descriptor: | GTP-dependent dephospho-CoA kinase | | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | | Deposit date: | 2023-06-28 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92, 2024
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