2D6N
| Crystal structure of mouse galectin-9 N-terminal CRD in complex with N-acetyllactosamine | Descriptor: | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, lectin, galactose binding, ... | Authors: | Nagae, M, Nishi, N, Nakamura, T, Murata, T, Wakatsuki, S, Kato, R. | Deposit date: | 2005-11-14 | Release date: | 2006-09-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition J.Biol.Chem., 281, 2006
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2D7C
| Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Shiba, T, Koga, H, Shin, H.W, Kawasaki, M, Kato, R, Nakayama, K, Wakatsuki, S. | Deposit date: | 2005-11-16 | Release date: | 2006-09-26 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1. Proc.Natl.Acad.Sci.Usa, 103, 2006
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2D6P
| Crystal structure of mouse galectin-9 N-terminal CRD in complex with T-antigen | Descriptor: | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose, lectin, galactose binding, ... | Authors: | Nagae, M, Nishi, N, Nakamura, T, Murata, T, Wakatsuki, S, Kato, R. | Deposit date: | 2005-11-14 | Release date: | 2006-09-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition J.Biol.Chem., 281, 2006
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2D6O
| Crystal structure of mouse galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer | Descriptor: | GLYCEROL, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, lectin, ... | Authors: | Nagae, M, Nishi, N, Nakamura, T, Murata, T, Wakatsuki, S, Kato, R. | Deposit date: | 2005-11-14 | Release date: | 2006-09-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition J.Biol.Chem., 281, 2006
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2DUO
| Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+-bound form | Descriptor: | CALCIUM ION, CHLORIDE ION, Vesicular integral-membrane protein VIP36 | 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 (1.8 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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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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2DUQ
| Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form | Descriptor: | CALCIUM ION, CHLORIDE ION, Vesicular integral-membrane protein VIP36, ... | 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 (1.8 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: | 2021-11-10 | 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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2EFC
| Ara7-GDP/AtVps9a | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Similarity to vacuolar protein sorting-associated protein VPS9, Small GTP-binding protein-like | Authors: | Uejima, T, Ihara, K, Goh, T, Ito, E, Sunada, M, Ueda, T, Nakano, A, Wakatsuki, S. | Deposit date: | 2007-02-22 | Release date: | 2008-02-26 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system J.Biol.Chem., 285, 2010
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2E3P
| Crystal structure of CERT START domain in complex with C16-cearmide (P1) | Descriptor: | 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 (1.4 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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2E3M
| Crystal structure of CERT START domain | 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 (2.2 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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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: | 2021-11-10 | 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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2EFH
| Ara7-GDP/AtVps9a(D185N) | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Similarity to vacuolar protein sorting-associated protein VPS9, Small GTP-binding protein-like | Authors: | Ihara, K, Uejima, T, Wakatsuki, S. | Deposit date: | 2007-02-22 | Release date: | 2008-02-26 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system J.Biol.Chem., 285, 2010
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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: | 2011-07-13 | 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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2EFD
| Ara7/AtVps9a | Descriptor: | Similarity to vacuolar protein sorting-associated protein VPS9, Small GTP-binding protein-like | Authors: | Uejima, T, Ihara, K, Wakatsuki, S. | Deposit date: | 2007-02-22 | Release date: | 2008-02-26 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system J.Biol.Chem., 285, 2010
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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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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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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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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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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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2EFE
| Ara7-GDPNH2/AtVps9a | Descriptor: | AMINOPHOSPHONIC ACID-GUANYLATE ESTER, Similarity to vacuolar protein sorting-associated protein VPS9, Small GTP-binding protein-like | Authors: | Ihara, K, Uejima, T, Wakatsuki, S. | Deposit date: | 2007-02-22 | Release date: | 2008-02-26 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.08 Å) | Cite: | GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system J.Biol.Chem., 285, 2010
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5JD2
| SFX structure of corestreptavidin-selenobiotin complex | Descriptor: | 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid, Streptavidin | Authors: | DeMirci, H, Hunter, M.S, Boutet, S. | Deposit date: | 2016-04-15 | Release date: | 2016-11-16 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nat Commun, 7, 2016
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