1YIQ
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![BU of 1yiq by Molmil](/molmil-images/mine/1yiq) | Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADHIIG from Pseudomonas putida HK5. Compariison to the other quinohemoprotein alcohol dehydrogenase ADHIIB found in the same microorganism. | 分子名称: | CALCIUM ION, HEME C, PYRROLOQUINOLINE QUINONE, ... | 著者 | Toyama, H, Chen, Z.W, Fukumoto, M, Adachi, O, Matsushita, K, Mathews, F.S. | 登録日 | 2005-01-12 | 公開日 | 2005-08-16 | 最終更新日 | 2023-08-23 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5 J.Mol.Biol., 352, 2005
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1KEG
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![BU of 1keg by Molmil](/molmil-images/mine/1keg) | Antibody 64M-2 Fab complexed with dTT(6-4)TT | 分子名称: | 5'-D(*TP*(64T)P*TP*T)-3', Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain), ... | 著者 | Yokoyama, H, Mizutani, R, Satow, Y, Sato, K, Komatsu, Y, Ohtsuka, E, Nikaido, O. | 登録日 | 2001-11-15 | 公開日 | 2002-11-15 | 最終更新日 | 2023-08-16 | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | 主引用文献 | Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides. Acta Crystallogr.,Sect.D, 68, 2012
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4EVD
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![BU of 4evd by Molmil](/molmil-images/mine/4evd) | Crystal Structure HP-NAP from strain YS29 cadmium loaded (Cocrystallization 50mM) | 分子名称: | CADMIUM ION, Neutrophil-activating protein | 著者 | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | 登録日 | 2012-04-26 | 公開日 | 2012-06-27 | 最終更新日 | 2023-11-08 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form Biochem.Biophys.Res.Commun., 422, 2012
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4EVE
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![BU of 4eve by Molmil](/molmil-images/mine/4eve) | Crystal Structure HP-NAP from strain YS29 in apo form | 分子名称: | Neutrophil-activating protein, SULFATE ION | 著者 | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | 登録日 | 2012-04-26 | 公開日 | 2012-06-27 | 最終更新日 | 2023-11-08 | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | 主引用文献 | Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form Biochem.Biophys.Res.Commun., 422, 2012
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4EVC
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![BU of 4evc by Molmil](/molmil-images/mine/4evc) | Crystal Structure HP-NAP from strain YS39 cadmium loaded (Cocrystallization 50mM) | 分子名称: | CADMIUM ION, Neutrophil-activating protein | 著者 | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | 登録日 | 2012-04-26 | 公開日 | 2012-06-27 | 最終更新日 | 2023-11-08 | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | 主引用文献 | Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form Biochem.Biophys.Res.Commun., 422, 2012
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4EVB
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![BU of 4evb by Molmil](/molmil-images/mine/4evb) | Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM) | 分子名称: | 1,2-ETHANEDIOL, Neutrophil-activating protein, SULFATE ION, ... | 著者 | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | 登録日 | 2012-04-26 | 公開日 | 2012-06-27 | 最終更新日 | 2023-11-08 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form Biochem.Biophys.Res.Commun., 422, 2012
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6IDG
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![BU of 6idg by Molmil](/molmil-images/mine/6idg) | antibody 64M-5 Fab in complex with dT(6-4)T | 分子名称: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), DNA (5'-D(*(64T)P*(5PY))-3') | 著者 | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | 登録日 | 2018-09-10 | 公開日 | 2019-02-13 | 最終更新日 | 2023-11-22 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms. Acta Crystallogr.,Sect.F, 75, 2019
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6IDH
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![BU of 6idh by Molmil](/molmil-images/mine/6idh) | Antibody 64M-5 Fab in ligand-free form | 分子名称: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) | 著者 | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | 登録日 | 2018-09-10 | 公開日 | 2019-02-13 | 最終更新日 | 2023-11-22 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms. Acta Crystallogr.,Sect.F, 75, 2019
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1EHL
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![BU of 1ehl by Molmil](/molmil-images/mine/1ehl) | 64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T | 分子名称: | 5'-(D(5HT)P*(6-4)T)-3', ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (HEAVY CHAIN), ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (LIGHT CHAIN) | 著者 | Yokoyama, H, Mizutani, R, Satow, Y, Komatsu, Y, Ohtsuka, E, Nikaido, O. | 登録日 | 2000-02-21 | 公開日 | 2001-02-21 | 最終更新日 | 2011-07-13 | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | 主引用文献 | Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation. J.Mol.Biol., 299, 2000
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6M4B
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![BU of 6m4b by Molmil](/molmil-images/mine/6m4b) | |
5ZO7
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![BU of 5zo7 by Molmil](/molmil-images/mine/5zo7) | Kinesin spindle protein Eg5 in complex with STLC-type inhibitor PVEI0138 | 分子名称: | (2R)-2-azanyl-3-[[2-(4-methoxyphenyl)-2-tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3,5,7,12,14-hexaenyl]sulfanyl]propanoic acid, ADENOSINE-5'-DIPHOSPHATE, Kinesin-like protein KIF11, ... | 著者 | Yokoyama, H, Sato, K. | 登録日 | 2018-04-12 | 公開日 | 2018-10-10 | 最終更新日 | 2024-03-27 | 実験手法 | X-RAY DIFFRACTION (2.6 Å) | 主引用文献 | Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. Acs Omega, 3, 2018
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5ZO8
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![BU of 5zo8 by Molmil](/molmil-images/mine/5zo8) | |
5ZO9
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![BU of 5zo9 by Molmil](/molmil-images/mine/5zo9) | Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (C2 type) | 分子名称: | (2R)-2-azanyl-3-[(4-methoxyphenyl)-diphenyl-methyl]sulfanyl-propanoic acid, ADENOSINE-5'-DIPHOSPHATE, Kinesin-like protein KIF11, ... | 著者 | Yokoyama, H, Sato, K. | 登録日 | 2018-04-12 | 公開日 | 2018-10-10 | 最終更新日 | 2024-03-27 | 実験手法 | X-RAY DIFFRACTION (2.7 Å) | 主引用文献 | Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. Acs Omega, 3, 2018
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6KDH
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![BU of 6kdh by Molmil](/molmil-images/mine/6kdh) | Antibody 64M-5 Fab including isoAsp in ligand-free form | 分子名称: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) | 著者 | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | 登録日 | 2019-07-02 | 公開日 | 2019-12-18 | 最終更新日 | 2023-11-22 | 実験手法 | X-RAY DIFFRACTION (2.47 Å) | 主引用文献 | Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab. Sci Rep, 9, 2019
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3BK6
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![BU of 3bk6 by Molmil](/molmil-images/mine/3bk6) | |
3BPP
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![BU of 3bpp by Molmil](/molmil-images/mine/3bpp) | |
6KDI
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![BU of 6kdi by Molmil](/molmil-images/mine/6kdi) | Antibody 64M-5 Fab including isoAsp in complex with dT(6-4)T | 分子名称: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), DNA (5'-D(*(64T)P*(5PY))-3') | 著者 | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | 登録日 | 2019-07-02 | 公開日 | 2019-12-18 | 最終更新日 | 2023-11-22 | 実験手法 | X-RAY DIFFRACTION (2.7 Å) | 主引用文献 | Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab. Sci Rep, 9, 2019
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7FI3
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![BU of 7fi3 by Molmil](/molmil-images/mine/7fi3) | Archaeal oligopeptide permease A (OppA) from Thermococcus kodakaraensis in complex with an endogenous pentapeptide | 分子名称: | ABC-type dipeptide/oligopeptide transport system, GLYCEROL, HEXAETHYLENE GLYCOL, ... | 著者 | Yokoyama, H, Kamei, N, Konishi, K, Hara, K, Hashimoto, H. | 登録日 | 2021-07-30 | 公開日 | 2022-04-13 | 最終更新日 | 2022-06-22 | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | 主引用文献 | Structural basis for peptide recognition by archaeal oligopeptide permease A. Proteins, 90, 2022
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3VIV
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![BU of 3viv by Molmil](/molmil-images/mine/3viv) | 1510-N membrane-bound stomatin-specific protease K138A mutant in complex with a substrate peptide | 分子名称: | 441aa long hypothetical nfeD protein, CHLORIDE ION, GLYCEROL, ... | 著者 | Yokoyama, H, Matsui, I, Fujii, S. | 登録日 | 2011-10-12 | 公開日 | 2012-05-23 | 最終更新日 | 2023-11-08 | 実験手法 | X-RAY DIFFRACTION (2.25 Å) | 主引用文献 | Crystal structure of a membrane stomatin-specific protease in complex with a substrate Peptide Biochemistry, 51, 2012
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3VW3
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![BU of 3vw3 by Molmil](/molmil-images/mine/3vw3) | Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct | 分子名称: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), COBALT HEXAMMINE(III), ... | 著者 | Yokoyama, H, Mizutani, R, Satow, Y. | 登録日 | 2012-07-30 | 公開日 | 2013-03-27 | 最終更新日 | 2023-11-08 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab Acta Crystallogr.,Sect.D, 69, 2013
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3ABL
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![BU of 3abl by Molmil](/molmil-images/mine/3abl) | Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset) | 分子名称: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | 著者 | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | 登録日 | 2009-12-16 | 公開日 | 2010-01-19 | 最終更新日 | 2023-11-01 | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | 主引用文献 | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump Proc.Natl.Acad.Sci.USA, 106, 2009
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3ABM
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![BU of 3abm by Molmil](/molmil-images/mine/3abm) | Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset) | 分子名称: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | 著者 | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | 登録日 | 2009-12-16 | 公開日 | 2010-01-19 | 最終更新日 | 2023-11-01 | 実験手法 | X-RAY DIFFRACTION (1.95 Å) | 主引用文献 | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump Proc.Natl.Acad.Sci.USA, 106, 2009
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2ZXW
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![BU of 2zxw by Molmil](/molmil-images/mine/2zxw) | Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset) | 分子名称: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | 著者 | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Hirata, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | 登録日 | 2009-01-08 | 公開日 | 2009-02-24 | 最終更新日 | 2023-11-01 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump Proc.Natl.Acad.Sci.USA, 106, 2009
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3WPN
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![BU of 3wpn by Molmil](/molmil-images/mine/3wpn) | |
7WXS
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![BU of 7wxs by Molmil](/molmil-images/mine/7wxs) | Lysozyme protected by polyacrylamide gel | 分子名称: | CHLORIDE ION, GLYCEROL, Lysozyme C, ... | 著者 | Muroyama, H, Tomoike, F, Nagae, T, Okada, T. | 登録日 | 2022-02-15 | 公開日 | 2023-02-22 | 最終更新日 | 2023-11-29 | 実験手法 | X-RAY DIFFRACTION (1.25 Å) | 主引用文献 | Post-crystallization protection of protein crystals by polyacrylamide To Be Published
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