1VGN
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![BU of 1vgn by Molmil](/molmil-images/mine/1vgn) | Structure-based design of the irreversible inhibitors to metallo--lactamase (IMP-1) | Descriptor: | 3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE, ACETIC ACID, Beta-lactamase IMP-1, ... | Authors: | Kurosaki, H, Yamaguchi, Y, Higashi, T, Soga, K, Matsueda, S, Misumi, S, Yamagata, Y, Arakawa, Y, Goto, M. | Deposit date: | 2004-04-27 | Release date: | 2005-06-21 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.63 Å) | Cite: | Irreversible Inhibition of Metallo-beta-lactamase (IMP-1) by 3-(3-Mercaptopropionylsulfanyl)propionic Acid Pentafluorophenyl Ester Angew.Chem.Int.Ed.Engl., 44, 2005
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1WRD
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![BU of 1wrd by Molmil](/molmil-images/mine/1wrd) | Crystal structure of Tom1 GAT domain in complex with ubiquitin | Descriptor: | Target of Myb protein 1, Ubiquitin | Authors: | Akutsu, M, Kawasaki, M, Katoh, Y, Shiba, T, Yamaguchi, Y, Kato, R, Kato, K, Nakayama, K, Wakatsuki, S. | Deposit date: | 2004-10-14 | Release date: | 2005-10-11 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. Febs Lett., 579, 2005
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1UMI
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![BU of 1umi by Molmil](/molmil-images/mine/1umi) | Structural basis of sugar-recognizing ubiquitin ligase | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose, F-box only protein 2 | Authors: | Mizushima, T, Hirao, T, Yoshida, Y, Lee, S.J, Chiba, T, Iwai, K, Yamaguchi, Y, Kato, K, Tsukihara, T, Tanaka, K. | Deposit date: | 2003-10-01 | Release date: | 2004-04-06 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis of sugar-recognizing ubiquitin ligase. Nat.Struct.Mol.Biol., 11, 2004
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5AV7
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![BU of 5av7 by Molmil](/molmil-images/mine/5av7) | Crystal structure of Calsepa lectin in complex with bisected glycan | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside, Lectin | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2015-06-12 | Release date: | 2016-04-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins Sci Rep, 6, 2016
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1UMH
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![BU of 1umh by Molmil](/molmil-images/mine/1umh) | Structural basis of sugar-recognizing ubiquitin ligase | Descriptor: | F-box only protein 2, NICKEL (II) ION | Authors: | Mizushima, T, Hirao, T, Yoshida, Y, Lee, S.J, Chiba, T, Iwai, K, Yamaguchi, Y, Kato, K, Tsukihara, T, Tanaka, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-10-01 | Release date: | 2004-04-06 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural basis of sugar-recognizing ubiquitin ligase NAT.STRUCT.MOL.BIOL., 11, 2004
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1IYF
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![BU of 1iyf by Molmil](/molmil-images/mine/1iyf) | Solution structure of ubiquitin-like domain of human parkin | Descriptor: | parkin | Authors: | Sakata, E, Yamaguchi, Y, Kurimoto, E, Kikuchi, J, Yokoyama, S, Kawahara, H, Yokosawa, H, Hattori, N, Mizuno, Y, Tanaka, K, Kato, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2002-08-13 | Release date: | 2003-03-25 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain EMBO REP., 4, 2003
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5B1W
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5AZW
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![BU of 5azw by Molmil](/molmil-images/mine/5azw) | Crystal structure of p24beta1 GOLD domain | Descriptor: | 1,2-ETHANEDIOL, Transmembrane emp24 domain-containing protein 2 | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2015-10-23 | Release date: | 2016-09-14 | Last modified: | 2020-02-26 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | 3D Structure and Interaction of p24 beta and p24 delta Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport J.Mol.Biol., 428, 2016
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5AZY
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![BU of 5azy by Molmil](/molmil-images/mine/5azy) | Crystal structure of p24delta1 GOLD domain (Native 2) | Descriptor: | 1,2-ETHANEDIOL, SULFATE ION, Transmembrane emp24 domain-containing protein 10 | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2015-10-23 | Release date: | 2016-09-14 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | 3D Structure and Interaction of p24 beta and p24 delta Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport J.Mol.Biol., 428, 2016
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5B1X
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5AZX
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![BU of 5azx by Molmil](/molmil-images/mine/5azx) | Crystal structure of p24delta1 GOLD domain (native 1) | Descriptor: | SULFATE ION, Transmembrane emp24 domain-containing protein 10 | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2015-10-23 | Release date: | 2016-09-14 | Last modified: | 2020-02-26 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | 3D Structure and Interaction of p24 beta and p24 delta Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport J.Mol.Biol., 428, 2016
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1WZ1
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![BU of 1wz1 by Molmil](/molmil-images/mine/1wz1) | Crystal structure of the Fv fragment complexed with dansyl-lysine | Descriptor: | Ig heavy chain, Ig light chain, N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE | Authors: | Nakasako, M, Oka, T, Mashumo, M, Takahashi, H, Shimada, I, Yamaguchi, Y, Kato, K, Arata, Y. | Deposit date: | 2005-02-21 | Release date: | 2006-01-31 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten J.Mol.Biol., 351, 2005
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1WR6
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![BU of 1wr6 by Molmil](/molmil-images/mine/1wr6) | Crystal structure of GGA3 GAT domain in complex with ubiquitin | Descriptor: | ADP-ribosylation factor binding protein GGA3, ubiquitin | Authors: | Kawasaki, M, Shiba, T, Shiba, Y, Yamaguchi, Y, Matsugaki, N, Igarashi, N, Suzuki, M, Kato, R, Kato, K, Nakayama, K, Wakatsuki, S. | Deposit date: | 2004-10-12 | Release date: | 2005-06-28 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Molecular mechanism of ubiquitin recognition by GGA3 GAT domain. Genes Cells, 10, 2005
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1WXS
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![BU of 1wxs by Molmil](/molmil-images/mine/1wxs) | Solution Structure of Ufm1, a ubiquitin-fold modifier | Descriptor: | Ubiquitin-fold Modifier 1 | Authors: | Sasakawa, H, Sakata, E, Yamaguchi, Y, Komatsu, M, Tatsumi, K, Kominami, E, Tanaka, K, Kato, K. | Deposit date: | 2005-02-01 | Release date: | 2006-04-18 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1 Biochem.Biophys.Res.Commun., 343, 2006
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5ZIC
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![BU of 5zic by Molmil](/molmil-images/mine/5zic) | Crystal structure of human GnT-V luminal domain in complex with acceptor sugar | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-6-thio-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose, Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2018-03-14 | Release date: | 2018-08-01 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V. Nat Commun, 9, 2018
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5ZIB
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![BU of 5zib by Molmil](/molmil-images/mine/5zib) | Crystal structure of human GnT-V luminal domain in apo form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A | Authors: | Nagae, M, Yamaguchi, Y. | Deposit date: | 2018-03-14 | Release date: | 2018-08-01 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V. Nat Commun, 9, 2018
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2DOO
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![BU of 2doo by Molmil](/molmil-images/mine/2doo) | The structure of IMP-1 complexed with the detecting reagent (DansylC4SH) by a fluorescent probe | Descriptor: | BETA-LACTAMASE IMP-1, N-[4-({[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}AMINO)BUTYL]-3-SULFANYLPROPANAMIDE, ZINC ION | Authors: | Kurosaki, H, Yamaguchi, Y, Yasuzawa, H, Jin, W, Yamagata, Y, Arakawa, Y. | Deposit date: | 2006-05-01 | Release date: | 2006-11-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.43 Å) | Cite: | Probing, inhibition, and crystallographic characterization of metallo-beta-lactamase (IMP-1) with fluorescent agents containing dansyl and thiol groups Chemmedchem, 1, 2006
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5X1B
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![BU of 5x1b by Molmil](/molmil-images/mine/5x1b) | CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center | 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: | Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | Deposit date: | 2017-01-25 | Release date: | 2017-08-09 | Last modified: | 2017-12-06 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase. Sci Adv, 3, 2017
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5X19
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![BU of 5x19 by Molmil](/molmil-images/mine/5x19) | CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center | 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: | Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | Deposit date: | 2017-01-25 | Release date: | 2017-08-09 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase. Sci Adv, 3, 2017
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5X1F
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![BU of 5x1f by Molmil](/molmil-images/mine/5x1f) | CO bound cytochrome c oxidase without pump laser irradiation at 278K | 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: | Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | Deposit date: | 2017-01-25 | Release date: | 2017-08-09 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase. Sci Adv, 3, 2017
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3VY6
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![BU of 3vy6 by Molmil](/molmil-images/mine/3vy6) | |
2D5U
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3VZF
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2DPF
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![BU of 2dpf by Molmil](/molmil-images/mine/2dpf) | Crystal Structure of curculin1 homodimer | Descriptor: | Curculin, SULFATE ION | Authors: | Kurimoto, E, Suzuki, M, Amemiya, E, Yamaguchi, Y, Nirasawa, S, Shimba, N, Xu, N, Kashiwagi, T, Kawai, M, Suzuki, E, Kato, K. | Deposit date: | 2006-05-11 | Release date: | 2007-05-15 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Curculin Exhibits Sweet-tasting and Taste-modifying Activities through Its Distinct Molecular Surfaces. J.Biol.Chem., 282, 2007
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3VZG
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![BU of 3vzg by Molmil](/molmil-images/mine/3vzg) | |