2DX5
 
 | | The complex structure between the mouse EAP45-GLUE domain and ubiquitin | | Descriptor: | Ubiquitin, Vacuolar protein sorting protein 36 | | Authors: | Hirano, S, Suzuki, N, Slagsvold, T, Kawasaki, M, Trambaiolo, D, Kato, R, Stenmark, H, Wakatsuki, S. | | Deposit date: | 2006-08-24 | | Release date: | 2006-10-10 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.35 Å) | | Cite: | Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain
Nat.Struct.Mol.Biol., 13, 2006
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2EAE
 | | Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products | | Descriptor: | Alpha-fucosidase, CALCIUM ION, alpha-L-fucopyranose, ... | | Authors: | Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R. | | Deposit date: | 2007-01-31 | | Release date: | 2007-04-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
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2D0J
 | | Crystal Structure of Human GlcAT-S Apo Form | | Descriptor: | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 | | Authors: | Shiba, T, Kakuda, S, Ishiguro, M, Oka, S, Kawasaki, T, Wakatsuki, S, Kato, R. | | Deposit date: | 2005-08-03 | | Release date: | 2006-07-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope
To be published
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2EAB
 | | Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form) | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Alpha-fucosidase, ... | | Authors: | Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R. | | Deposit date: | 2007-01-31 | | Release date: | 2007-04-24 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.12 Å) | | Cite: | Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
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2E3N
 | | Crystal structure of CERT START domain in complex with C6-ceramide (P212121) | | Descriptor: | Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE | | Authors: | Kudo, N, Kumagai, K, Wakatsuki, S, Nishijima, M, Hanada, K, Kato, R. | | Deposit date: | 2006-11-28 | | Release date: | 2007-12-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2D3G
 | | Double sided ubiquitin binding of Hrs-UIM | | Descriptor: | ubiquitin, ubiquitin interacting motif from hepatocyte growth factor-regulated tyrosine kinase substrate | | Authors: | Hirano, S, Kawasaki, M, Kato, R, Wakatsuki, S. | | Deposit date: | 2005-09-28 | | Release date: | 2005-12-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting
Nat.Struct.Mol.Biol., 13, 2006
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2E3R
 | | Crystal structure of CERT START domain in complex with C18-ceramide (P1) | | Descriptor: | Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE | | Authors: | Kudo, N, Kumagai, K, Wakatsuki, S, Nishijima, M, Hanada, K, Kato, R. | | Deposit date: | 2006-11-28 | | Release date: | 2007-12-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2E6V
 | | Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man3GlcNAc-bound form | | Descriptor: | CALCIUM ION, Vesicular integral-membrane protein VIP36, alpha-D-mannopyranose, ... | | Authors: | Satoh, T, Kato, R, Wakatsuki, S. | | Deposit date: | 2007-01-04 | | Release date: | 2007-07-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36
J.Biol.Chem., 282, 2007
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2E3S
 | | Crystal structure of CERT START domain co-crystallized with C24-ceramide (P21) | | Descriptor: | Lipid-transfer protein CERT | | Authors: | Kudo, N, Kumagai, K, Wakatsuki, S, Nishijima, M, Hanada, K, Kato, R. | | Deposit date: | 2006-11-28 | | Release date: | 2007-12-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2EAC
 | | Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin | | Descriptor: | (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL, Alpha-fucosidase, CALCIUM ION | | Authors: | Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R. | | Deposit date: | 2007-01-31 | | Release date: | 2007-04-24 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
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2EAL
 | | Crystal structure of human galectin-9 N-terminal CRD in complex with Forssman pentasaccharide | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose, Galectin-9 | | Authors: | Nagae, M, Nakamura-Tsuruta, S, Nishi, N, Nakamura, T, Hirabayashi, J, Wakatsuki, S, Kato, R. | | Deposit date: | 2007-01-31 | | Release date: | 2007-09-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue.
J.Mol.Biol., 375, 2008
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2E3O
 | | Crystal structure of CERT START domain in complex with C16-ceramide (P212121) | | Descriptor: | DIMETHYL SULFOXIDE, Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE | | Authors: | Kudo, N, Kumagai, K, Wakatsuki, S, Nishijima, M, Hanada, K, Kato, R. | | Deposit date: | 2006-11-28 | | Release date: | 2007-12-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2EAK
 | | Crystal structure of human galectin-9 N-terminal CRD in complex with lactose | | Descriptor: | (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL, GLYCEROL, Galectin-9, ... | | Authors: | Nagae, M, Nakamura-Tsuruta, S, Nishi, N, Nakamura, T, Hirabayashi, J, Wakatsuki, S, Kato, R. | | Deposit date: | 2007-01-31 | | Release date: | 2007-09-25 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.97 Å) | | Cite: | Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue.
J.Mol.Biol., 375, 2008
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2F10
 | | Crystal Structure of the Human Sialidase Neu2 in Complex with Peramivir inhibitor | | Descriptor: | 3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID, PHOSPHATE ION, Sialidase 2 | | Authors: | Chavas, L.M.G, Kato, R, McKimm-Breschkin, J, Colman, P.M, Fusi, P, Tringali, C, Venerando, B, Tettamanti, G, Monti, E, Wakatsuki, S. | | Deposit date: | 2005-11-14 | | Release date: | 2006-11-21 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal Structure of the Human Sialidase Neu2 in Complex with Peramivir inhibitor
To be Published
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2F13
 | | Crystal Structure of the Human Sialidase Neu2 in Complex with 2',3'- dihydroxypropyl ether mimetic Inhibitor | | Descriptor: | (2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid, PHOSPHATE ION, Sialidase 2 | | Authors: | Chavas, L.M.G, Kato, R, Mann, M.C, Thomson, R.J, Dyason, J.C, von Itzstein, M, Fusi, P, Tringali, C, Venerando, B, Tettamanti, G, Monti, E, Wakatsuki, S. | | Deposit date: | 2005-11-14 | | Release date: | 2006-11-21 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | Crystal Structure of the Human Sialidase Neu2 in Complex with 2',3'- dihydroxypropyl ether mimetic Inhibitor
To be Published
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2DUR
 | | Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Satoh, T, Cowieson, N.P, Kato, R, Wakatsuki, S. | | Deposit date: | 2006-07-25 | | Release date: | 2007-07-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36
J.Biol.Chem., 282, 2007
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2DUP
 | | Crystal structure of VIP36 exoplasmic/lumenal domain, metal-free form | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Satoh, T, Cowieson, N.P, Kato, R, Wakatsuki, S. | | Deposit date: | 2006-07-25 | | Release date: | 2007-07-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36
J.Biol.Chem., 282, 2007
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2E3Q
 | | Crystal structure of CERT START domain in complex with C18-ceramide (P212121) | | Descriptor: | DIMETHYL SULFOXIDE, Lipid-transfer protein CERT, N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE | | Authors: | Kudo, N, Kumagai, K, Wakatsuki, S, Nishijima, M, Hanada, K, Kato, R. | | Deposit date: | 2006-11-28 | | Release date: | 2007-12-18 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.08 Å) | | Cite: | Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2EAD
 | | Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with substrate | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Alpha-fucosidase, CALCIUM ION, ... | | Authors: | Nagae, M, Tsuchiya, A, Katayama, T, Yamamoto, K, Wakatsuki, S, Kato, R. | | Deposit date: | 2007-01-31 | | Release date: | 2007-04-24 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282, 2007
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2F11
 | | Crystal Structure of the Human Sialidase Neu2 in Complex with isobutyl ether mimetic Inhibitor | | Descriptor: | 2-methylpropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid, PHOSPHATE ION, Sialidase 2 | | Authors: | Chavas, L.M.G, Kato, R, Mann, M.C, Thomson, R.J, Dyason, J.C, von Itzstein, M, Fusi, P, Tringali, C, Venerando, B, Tettamanti, G, Monti, E, Wakatsuki, S. | | Deposit date: | 2005-11-14 | | Release date: | 2006-11-21 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.57 Å) | | Cite: | Crystal Structure of the Human Sialidase Neu2 in Complex with isobutyl ether mimetic Inhibitor
To be Published
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2F26
 | | Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double Mutant | | Descriptor: | CHLORIDE ION, Sialidase 2 | | Authors: | Chavas, L.M.G, Kato, R, Fusi, P, Tringali, C, Venerando, B, Tettamanti, G, Monti, E, Wakatsuki, S. | | Deposit date: | 2005-11-15 | | Release date: | 2006-11-21 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double Mutant
To be Published
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2Z44
 | | Crystal Structure of Selenomethionine-labeled ORF134 | | Descriptor: | ORF134 | | Authors: | Tomimoto, Y, Ihara, K, Onizuka, T, Kanai, S, Ashida, H, Yokota, A, Tanaka, S, Miyasaka, H, Yamada, Y, Kato, R, Wakatsuki, S. | | Deposit date: | 2007-06-12 | | Release date: | 2008-06-24 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal Structure of ORF134
To be Published
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2ZAM
 | | Crystal structure of mouse SKD1/VPS4B apo-form | | Descriptor: | Vacuolar protein sorting-associating protein 4B | | Authors: | Inoue, M, Kawasaki, M, Kamikubo, H, Kataoka, M, Kato, R, Yoshimori, T, Wakatsuki, S. | | Deposit date: | 2007-10-08 | | Release date: | 2008-10-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B
Traffic, 9, 2008
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2Z46
 | | Crystal Structure of Native-ORF134 | | Descriptor: | ORF134 | | Authors: | Tomimoto, Y, Ihara, K, Onizuka, T, Kanai, S, Ashida, H, Yokota, A, Tanaka, S, Miyasaka, H, Yamada, Y, Kato, R, Wakatsuki, S. | | Deposit date: | 2007-06-12 | | Release date: | 2008-06-24 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.97 Å) | | Cite: | Crystal Structure of ORF134
To be Published
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2Z9Z
 | | Crystal structure of CERT START domain(N504A mutant), in complex with C10-diacylglycerol | | Descriptor: | (2S)-3-hydroxypropane-1,2-diyl didecanoate, Lipid-transfer protein CERT | | Authors: | Kudo, N, Kumagai, K, Wakatsuki, S, Nishijima, M, Hanada, K, Kato, R. | | Deposit date: | 2007-09-26 | | Release date: | 2008-02-12 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.74 Å) | | Cite: | Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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