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9J7X
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BU of 9j7x by Molmil
Crystal structure of quintuple mutant C terminal fragment of Clostridium perfringens enterotoxin (C-CPEm19)
Descriptor: Heat-labile enterotoxin B chain
Authors:Aoyama, H.
Deposit date:2024-08-20
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structure of quintuple mutant C terminal fragment of Clostridium perfringens enterotoxin (C-CPEm19)
To Be Published
4EVD
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BU of 4evd by Molmil
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
4EVB
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BU of 4evb by Molmil
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
4EVE
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BU of 4eve by Molmil
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
4EVC
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BU of 4evc by Molmil
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
6M4B
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BU of 6m4b by Molmil
1510-N membrane-bound stomatin-specific protease S97A mutant
Descriptor: Membrane-bound protease PH1510, SULFATE ION
Authors:Yokoyama, H, Suzuki, K.
Deposit date:2020-03-06
Release date:2020-06-10
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Inactive dimeric structure of the protease domain of stomatin operon partner protein.
Acta Crystallogr.,Sect.D, 76, 2020
7FI3
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BU of 7fi3 by Molmil
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:2024-10-16
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural basis for peptide recognition by archaeal oligopeptide permease A.
Proteins, 90, 2022
6IDG
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BU of 6idg by Molmil
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:2024-10-09
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
6IDH
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BU of 6idh by Molmil
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:2024-10-09
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
6KDI
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BU of 6kdi by Molmil
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:2024-10-30
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
6KDH
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BU of 6kdh by Molmil
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:2024-11-20
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
1KEG
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BU of 1keg by Molmil
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:2024-11-20
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
5ZO9
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BU of 5zo9 by Molmil
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
5ZO7
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BU of 5zo7 by Molmil
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
5ZO8
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BU of 5zo8 by Molmil
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
3VIV
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BU of 3viv by Molmil
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
3VW3
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BU of 3vw3 by Molmil
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:2024-11-06
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
7WXT
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BU of 7wxt by Molmil
Thaumatin protected by polyacrylamide gel
Descriptor: GLYCEROL, L(+)-TARTARIC ACID, Thaumatin I
Authors:Muroyama, H, Tomoike, F, Nagae, T, Okada, T.
Deposit date:2022-02-15
Release date:2023-02-22
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Post-crystallization protection of protein crystals by polyacrylamide
To Be Published
7WXS
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BU of 7wxs by Molmil
Lysozyme protected by polyacrylamide gel
Descriptor: CHLORIDE ION, GLYCEROL, Lysozyme C, ...
Authors:Muroyama, H, Tomoike, F, Nagae, T, Okada, T.
Deposit date:2022-02-15
Release date:2023-02-22
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Post-crystallization protection of protein crystals by polyacrylamide
To Be Published
3WPN
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BU of 3wpn by Molmil
Kinesin spindle protein Eg5 in complex with ATP-competitive inhibitor PVZB1194
Descriptor: 3'-fluoro-4'-(trifluoromethyl)biphenyl-4-sulfonamide, Kinesin-like protein KIF11
Authors:Yokoyama, H, Katoh, S, Fujii, S.
Deposit date:2014-01-14
Release date:2015-01-21
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural basis of new allosteric inhibition in Kinesin spindle protein eg5
Acs Chem.Biol., 10, 2015
3WWV
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BU of 3wwv by Molmil
C-terminal domain of stomatin operon partner protein 1510-C from Pyrococcus horikoshii
Descriptor: SODIUM ION, Stomatin operon partner protein
Authors:Yokoyama, H, Matsui, I.
Deposit date:2014-06-30
Release date:2014-10-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of the stomatin operon partner protein from Pyrococcus horikoshii indicates the formation of a multimeric assembly
FEBS Open Bio, 4, 2014
3WG5
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BU of 3wg5 by Molmil
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
3BPP
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BU of 3bpp by Molmil
1510-N membrane protease K138A mutant specific for a stomatin homolog from Pyrococcus horikoshii
Descriptor: 1510-N membrane protease
Authors:Yokoyama, H, Hamamatsu, S, Fujii, S, Matsui, I.
Deposit date:2007-12-19
Release date:2008-04-29
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin
J.SYNCHROTRON RADIAT., 15, 2008
3BK6
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BU of 3bk6 by Molmil
Crystal structure of a core domain of stomatin from Pyrococcus horikoshii
Descriptor: PH stomatin
Authors:Yokoyama, H, Fujii, S, Matsui, I.
Deposit date:2007-12-05
Release date:2008-02-19
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold
J.Mol.Biol., 376, 2008
2ZXW
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BU of 2zxw by Molmil
Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset)
Descriptor: (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, ...
Authors:Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Hirata, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S.
Deposit date:2009-01-08
Release date:2009-02-24
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.5 Å)
Cite: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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