8J3T
 
 | | Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand | | Descriptor: | (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide, Assemblin | | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | | Deposit date: | 2023-04-18 | | Release date: | 2023-11-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
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1MGT
 | | CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1 | | Descriptor: | PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE), SULFATE ION | | Authors: | Hashimoto, H, Inoue, T, Nishioka, M, Fujiwara, S, Takagi, M, Imanaka, T, Kai, Y. | | Deposit date: | 1999-01-12 | | Release date: | 2000-01-07 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase.
J.Mol.Biol., 292, 1999
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8H3M
 | | Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy chain, Spike glycoprotein | | Authors: | Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y. | | Deposit date: | 2022-10-09 | | Release date: | 2023-05-10 | | Last modified: | 2023-08-02 | | Method: | ELECTRON MICROSCOPY (2.48 Å) | | Cite: | Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
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8H3N
 | | Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy-chain, MO1 light chain, ... | | Authors: | Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y. | | Deposit date: | 2022-10-09 | | Release date: | 2023-05-10 | | Last modified: | 2023-08-02 | | Method: | ELECTRON MICROSCOPY (2.73 Å) | | Cite: | Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
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5GUK
 | | Crystal structure of apo form of cyclolavandulyl diphosphate synthase (CLDS) from Streptomyces sp. CL190 | | Descriptor: | CHLORIDE ION, Cyclolavandulyl diphosphate synthase | | Authors: | Tomita, T, Kobayashi, M, Nishiyama, M, Kuzuyama, T. | | Deposit date: | 2016-08-29 | | Release date: | 2017-08-30 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase that Catalyzes Consecutive Condensation and Cyclization.
Angew. Chem. Int. Ed. Engl., 56, 2017
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5GUL
 | | Crystal structure of Tris/PPix2/Mg2+ bound form of cyclolavandulyl diphosphate synthase (CLDS) from Streptomyces sp. CL190 | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Cyclolavandulyl diphosphate synthase, MAGNESIUM ION, ... | | Authors: | Tomita, T, Kobayashi, M, Nishiyama, M, Kuzuyama, T. | | Deposit date: | 2016-08-29 | | Release date: | 2017-08-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.73 Å) | | Cite: | Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase that Catalyzes Consecutive Condensation and Cyclization.
Angew. Chem. Int. Ed. Engl., 56, 2017
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4YGE
 | | Crystal structure of ERGIC-53/MCFD2, trigonal calcium-bound form 2 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.05 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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4YGC
 | | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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4YGD
 | | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.51 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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4YGB
 | | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form | | Descriptor: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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1WZE
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4Y1P
 | | Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus acidocaldarius complex with 3-isopropylmalate and Mg2+ | | Descriptor: | 3-ISOPROPYLMALIC ACID, 3-isopropylmalate dehydrogenase, MAGNESIUM ION, ... | | Authors: | Takahashi, K, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2015-02-08 | | Release date: | 2016-03-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Characterization of two beta-decarboxylating dehydrogenases from Sulfolobus acidocaldarius
Extremophiles, 20, 2016
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5K2M
 | | Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA | | Descriptor: | 2-AMINOHEXANEDIOIC ACID, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2016-05-19 | | Release date: | 2016-09-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
J. Biol. Chem., 291, 2016
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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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1UC4
 | | Structure of diol dehydratase complexed with (S)-1,2-propanediol | | Descriptor: | AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ... | | Authors: | Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T. | | Deposit date: | 2003-04-08 | | Release date: | 2003-07-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.BIOL.CHEM., 278, 2003
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1UC5
 | | Structure of diol dehydratase complexed with (R)-1,2-propanediol | | Descriptor: | AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ... | | Authors: | Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T. | | Deposit date: | 2003-04-08 | | Release date: | 2003-07-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.Biol.Chem., 278, 2003
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7C9R
 | | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970 | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene, Alpha subunit 1 of light-harvesting 1 complex, ... | | Authors: | Tani, K, Kanno, R, Makino, Y, Hall, M, Takenouchi, M, Imanishi, M, Yu, L.-J, Overmann, J, Madigan, M.T, Kimura, Y, Mizoguchi, A, Humbel, B.M, Wang-Otomo, Z.-Y. | | Deposit date: | 2020-06-07 | | Release date: | 2020-10-07 | | Last modified: | 2020-10-14 | | Method: | ELECTRON MICROSCOPY (2.82 Å) | | Cite: | Cryo-EM structure of a Ca 2+ -bound photosynthetic LH1-RC complex containing multiple alpha beta-polypeptides.
Nat Commun, 11, 2020
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2AOW
 | | Histamine Methyltransferase (Natural Variant I105) Complexed with the Acetylcholinesterase Inhibitor and Altzheimer's Disease Drug Tacrine | | Descriptor: | Histamine N-methyltransferase, TACRINE | | Authors: | Horton, J.R, Sawada, K, Nishibori, M, Cheng, X. | | Deposit date: | 2005-08-14 | | Release date: | 2005-09-13 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.97 Å) | | Cite: | Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
J.Mol.Biol., 353, 2005
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2AOX
 | | Histamine Methyltransferase (Primary Variant T105) Complexed with the Acetylcholinesterase Inhibitor and Altzheimer's Disease Drug Tacrine | | Descriptor: | Histamine N-methyltransferase, TACRINE | | Authors: | Horton, J.R, Sawada, K, Nishibori, M, Cheng, X. | | Deposit date: | 2005-08-14 | | Release date: | 2005-09-13 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (3.12 Å) | | Cite: | Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
J.Mol.Biol., 353, 2005
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2AOV
 | | Histamine Methyltransferase Complexed with the Antifolate Drug Metoprine | | Descriptor: | 4-(DIMETHYLAMINO)BUTYL IMIDOTHIOCARBAMATE, 5-(3,4-DICHLOROPHENYL)-6-METHYLPYRIMIDINE-2,4-DIAMINE, Histamine N-methyltransferase | | Authors: | Horton, J.R, Sawada, K, Nishibori, M, Cheng, X. | | Deposit date: | 2005-08-14 | | Release date: | 2005-09-13 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.48 Å) | | Cite: | Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
J.Mol.Biol., 353, 2005
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2AOU
 | | Histamine Methyltransferase Complexed with the Antimalarial Drug Amodiaquine | | Descriptor: | 4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL, Histamine N-methyltransferase | | Authors: | Horton, J.R, Sawada, K, Nishibori, M, Cheng, X. | | Deposit date: | 2005-08-14 | | Release date: | 2005-09-13 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
J.Mol.Biol., 353, 2005
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2AOT
 | | Histamine Methyltransferase Complexed with the Antihistamine Drug Diphenhydramine | | Descriptor: | Histamine N-methyltransferase, N-[2-(BENZHYDRYLOXY)ETHYL]-N,N-DIMETHYLAMINE, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Horton, J.R, Sawada, K, Nishibori, M, Cheng, X. | | Deposit date: | 2005-08-14 | | Release date: | 2005-09-13 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
J.Mol.Biol., 353, 2005
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5X3D
 | | Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis | | Descriptor: | Phosphoenolpyruvate phosphomutase, [[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid | | Authors: | Tomita, T, Cho, S.H, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2017-02-04 | | Release date: | 2017-09-13 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme
ACS Chem. Biol., 12, 2017
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5XOY
 | | Crystal structure of LysK from Thermus thermophilus in complex with Lysine | | Descriptor: | LYSINE, SULFATE ION, [LysW]-lysine hydrolase | | Authors: | Tomita, T, Fujita, S, Hasebe, F, Cho, S.-H, Yoshida, A, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2017-05-31 | | Release date: | 2017-09-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW
Biochem. Biophys. Res. Commun., 491, 2017
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8GYH
 | | Crystal structure of Fic25 (apo form) from Streptomyces ficellus | | Descriptor: | DegT/DnrJ/EryC1/StrS family aminotransferase, GLYCEROL, IMIDAZOLE | | Authors: | Kurosawa, S, Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2022-09-22 | | Release date: | 2023-02-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.
Acs Chem.Biol., 18, 2023
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