3BK6
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6M4B
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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) | Descriptor: | CADMIUM ION, Neutrophil-activating protein | Authors: | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | Deposit date: | 2012-04-26 | Release date: | 2012-06-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | 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) | Descriptor: | CADMIUM ION, Neutrophil-activating protein | Authors: | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | Deposit date: | 2012-04-26 | Release date: | 2012-06-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | 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) | Descriptor: | 1,2-ETHANEDIOL, Neutrophil-activating protein, SULFATE ION, ... | Authors: | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | Deposit date: | 2012-04-26 | Release date: | 2012-06-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | 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 | Descriptor: | Neutrophil-activating protein, SULFATE ION | Authors: | Yokoyama, H, Tsuruta, O, Akao, N, Fujii, S. | Deposit date: | 2012-04-26 | Release date: | 2012-06-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | 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 | Descriptor: | 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') | Authors: | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | Deposit date: | 2018-09-10 | Release date: | 2019-02-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | 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 | Descriptor: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) | Authors: | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | Deposit date: | 2018-09-10 | Release date: | 2019-02-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | 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 | Descriptor: | 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) | Authors: | Yokoyama, H, Mizutani, R, Satow, Y, Komatsu, Y, Ohtsuka, E, Nikaido, O. | Deposit date: | 2000-02-21 | Release date: | 2001-02-21 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | 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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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 | Descriptor: | 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') | Authors: | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | Deposit date: | 2019-07-02 | Release date: | 2019-12-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | 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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6KDH
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![BU of 6kdh by Molmil](/molmil-images/mine/6kdh) | Antibody 64M-5 Fab including isoAsp in ligand-free form | Descriptor: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) | Authors: | Yokoyama, H, Mizutani, R, Noguchi, S, Hayashida, N. | Deposit date: | 2019-07-02 | Release date: | 2019-12-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.47 Å) | Cite: | 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 | Descriptor: | ABC-type dipeptide/oligopeptide transport system, GLYCEROL, HEXAETHYLENE GLYCOL, ... | Authors: | Yokoyama, H, Kamei, N, Konishi, K, Hara, K, Hashimoto, H. | Deposit date: | 2021-07-30 | Release date: | 2022-04-13 | Last modified: | 2022-06-22 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for peptide recognition by archaeal oligopeptide permease A. Proteins, 90, 2022
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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 | Descriptor: | 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), ... | Authors: | Yokoyama, H, Mizutani, R, Satow, Y, Sato, K, Komatsu, Y, Ohtsuka, E, Nikaido, O. | Deposit date: | 2001-11-15 | Release date: | 2002-11-15 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | 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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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) | Descriptor: | (2R)-2-azanyl-3-[(4-methoxyphenyl)-diphenyl-methyl]sulfanyl-propanoic acid, ADENOSINE-5'-DIPHOSPHATE, Kinesin-like protein KIF11, ... | Authors: | Yokoyama, H, Sato, K. | Deposit date: | 2018-04-12 | Release date: | 2018-10-10 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | 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) | Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (P21 type) | Descriptor: | (2R)-2-azanyl-3-[(4-methoxyphenyl)-diphenyl-methyl]sulfanyl-propanoic acid, ADENOSINE-5'-DIPHOSPHATE, Kinesin-like protein KIF11, ... | Authors: | Yokoyama, H, Sato, K. | Deposit date: | 2018-04-12 | Release date: | 2018-10-10 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | 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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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 | Descriptor: | (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, ... | Authors: | Yokoyama, H, Sato, K. | Deposit date: | 2018-04-12 | Release date: | 2018-10-10 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | 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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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 | Descriptor: | 441aa long hypothetical nfeD protein, CHLORIDE ION, GLYCEROL, ... | Authors: | Yokoyama, H, Matsui, I, Fujii, S. | Deposit date: | 2011-10-12 | Release date: | 2012-05-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | 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 | Descriptor: | Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), COBALT HEXAMMINE(III), ... | Authors: | Yokoyama, H, Mizutani, R, Satow, Y. | Deposit date: | 2012-07-30 | Release date: | 2013-03-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | 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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3WG5
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![BU of 3wg5 by Molmil](/molmil-images/mine/3wg5) | 1510-N membrane-bound stomatin-specific protease K138A mutant in complex with a substrate peptide under heat treatment | Descriptor: | 441aa long hypothetical nfeD protein, CHLORIDE ION, GLYCEROL, ... | Authors: | Yokoyama, H, Fujii, S, Matsui, I. | Deposit date: | 2013-07-26 | Release date: | 2013-10-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease. J.Synchrotron Radiat., 20, 2013
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3WWV
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3WPN
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3BPP
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![BU of 3bpp by Molmil](/molmil-images/mine/3bpp) | |
2DEO
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![BU of 2deo by Molmil](/molmil-images/mine/2deo) | |
3O59
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![BU of 3o59 by Molmil](/molmil-images/mine/3o59) | |
8GN9
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![BU of 8gn9 by Molmil](/molmil-images/mine/8gn9) | SPFH domain of Pyrococcus horikoshii stomatin | Descriptor: | SODIUM ION, Stomatin homolog PH1511 | Authors: | Komatsu, T, Matsui, I, Yokoyama, H. | Deposit date: | 2022-08-23 | Release date: | 2022-12-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural and mutational studies suggest key residues to determine whether stomatin SPFH domains form dimers or trimers. Biochem Biophys Rep, 32, 2022
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