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PDB: 75 results
2Z2T
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BU of 2z2t by Molmil
Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK
Descriptor: ACETIC ACID, Fusion inhibitor peptide SC34EK, SULFATE ION, ...
Authors:Nakamura, S, Ohkubo, T, Kobayashi, Y.
Deposit date:2007-05-28
Release date:2008-06-03
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Intrahelical Salt-bridges in a-Helical Peptide Enhances its Binding to the Target: A New Design for HIV-1 Fusion Inhibitors
To be Published
2AI5
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BU of 2ai5 by Molmil
Solution Structure of Cytochrome C552, determined by Distributed Computing Implementation for NMR data
Descriptor: Cytochrome c-552, HEME C
Authors:Nakamura, S, Ichiki, S.I, Takashima, H, Uchiyama, S, Hasegawa, J, Kobayashi, Y, Sambongi, Y, Ohkubo, T.
Deposit date:2005-07-29
Release date:2006-05-23
Last modified:2024-10-30
Method:SOLUTION NMR
Cite:Structure of Cytochrome c552 from a Moderate Thermophilic Bacterium, Hydrogenophilus thermoluteolus: Comparative Study on the Thermostability of Cytochrome c
Biochemistry, 45, 2006
8YVR
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BU of 8yvr by Molmil
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin
Descriptor: 1,2-ETHANEDIOL, 1-DEOXYNOJIRIMYCIN, Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2024-03-29
Release date:2025-03-19
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural insights into the inhibition mechanism of glucosidase inhibitors toward kojibiose hydrolase belonging to glycoside hydrolase family 65.
Biosci.Biotechnol.Biochem., 89, 2024
8YVS
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BU of 8yvs by Molmil
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with castanospermine
Descriptor: 1,2-ETHANEDIOL, CASTANOSPERMINE, Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2024-03-29
Release date:2025-03-19
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural insights into the inhibition mechanism of glucosidase inhibitors toward kojibiose hydrolase belonging to glycoside hydrolase family 65.
Biosci.Biotechnol.Biochem., 89, 2024
8IUA
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BU of 8iua by Molmil
Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltose
Descriptor: Candidate dextranase Glycoside hydrolase family 66, SODIUM ION, alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose, ...
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2023-03-24
Release date:2023-06-14
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
J.Biol.Chem., 299, 2023
8IU8
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BU of 8iu8 by Molmil
Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae
Descriptor: Candidate dextranase Glycoside hydrolase family 66, GLYCEROL
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2023-03-24
Release date:2023-06-14
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
J.Biol.Chem., 299, 2023
8IUB
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BU of 8iub by Molmil
Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltotriose
Descriptor: Candidate dextranase Glycoside hydrolase family 66, SODIUM ION, SULFATE ION, ...
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2023-03-24
Release date:2023-06-14
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.18 Å)
Cite:Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
J.Biol.Chem., 299, 2023
8IU9
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BU of 8iu9 by Molmil
Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with glucose
Descriptor: Candidate dextranase Glycoside hydrolase family 66, SODIUM ION, alpha-D-glucopyranose, ...
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2023-03-24
Release date:2023-06-14
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
J.Biol.Chem., 299, 2023
6AKF
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BU of 6akf by Molmil
Crystal structure of mouse claudin-3 P134A mutant in complex with C-terminal fragment of Clostridium perfringens enterotoxin
Descriptor: Claudin-3, Heat-labile enterotoxin B chain
Authors:Nakamura, S, Irie, K, Fujiyoshi, Y.
Deposit date:2018-08-31
Release date:2019-02-20
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (3.9 Å)
Cite:Morphologic determinant of tight junctions revealed by claudin-3 structures.
Nat Commun, 10, 2019
6AKG
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BU of 6akg by Molmil
Crystal structure of mouse claudin-3 P134G mutant in complex with C-terminal fragment of Clostridium perfringens enterotoxin
Descriptor: Claudin-3, Heat-labile enterotoxin B chain
Authors:Nakamura, S, Irie, K, Fujiyoshi, Y.
Deposit date:2018-08-31
Release date:2019-02-20
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (4.3 Å)
Cite:Morphologic determinant of tight junctions revealed by claudin-3 structures.
Nat Commun, 10, 2019
6AKE
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BU of 6ake by Molmil
Crystal structure of mouse claudin-3 in complex with C-terminal fragment of Clostridium perfringens enterotoxin
Descriptor: Claudin-3, Heat-labile enterotoxin B chain
Authors:Nakamura, S, Irie, K, Fujiyoshi, Y.
Deposit date:2018-08-31
Release date:2019-02-27
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Morphologic determinant of tight junctions revealed by claudin-3 structures.
Nat Commun, 10, 2019
8YDR
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BU of 8ydr by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce59, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDV
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BU of 8ydv by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDU
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BU of 8ydu by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDQ
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BU of 8ydq by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with Ce149
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide Ce149, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDP
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BU of 8ydp by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce9, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDT
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BU of 8ydt by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce41, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDW
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BU of 8ydw by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, SODIUM ION, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDS
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BU of 8yds by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce59, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8IUC
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BU of 8iuc by Molmil
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with isomaltose
Descriptor: 1,2-ETHANEDIOL, Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65, alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2023-03-24
Release date:2023-06-14
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
J.Biol.Chem., 299, 2023
7C95
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BU of 7c95 by Molmil
Crystal structure of the anti-human podoplanin antibody Fab fragment
Descriptor: GLYCEROL, Heavy chain of Fab fragment, Light chain of Fab fragment, ...
Authors:Nakamura, S, Suzuki, K, Ogasawara, S, Naruchi, K, Shimabukuro, J, Tukahara, N, Kaneko, M.K, Kato, Y, Murata, T.
Deposit date:2020-06-04
Release date:2020-09-30
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.
Biochem.Biophys.Res.Commun., 533, 2020
7FE4
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BU of 7fe4 by Molmil
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with glucose
Descriptor: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65, beta-D-glucopyranose
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2021-07-19
Release date:2021-11-10
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structure of a bacterial alpha-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases.
J.Biol.Chem., 297, 2021
2D0S
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BU of 2d0s by Molmil
Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus
Descriptor: HEME C, cytochrome c
Authors:Nakamura, S, Ichiki, S.I, Takashima, H, Uchiyama, S, Hasegawa, J, Kobayashi, Y, Sambongi, Y, Ohkubo, T.
Deposit date:2005-08-08
Release date:2006-05-23
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure of Cytochrome c552 from a Moderate Thermophilic Bacterium, Hydrogenophilus thermoluteolus: Comparative Study on the Thermostability of Cytochrome c
Biochemistry, 45, 2006
7FE3
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BU of 7fe3 by Molmil
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae
Descriptor: 1,2-ETHANEDIOL, Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
Authors:Nakamura, S, Miyazaki, T.
Deposit date:2021-07-19
Release date:2021-11-10
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Structure of a bacterial alpha-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases.
J.Biol.Chem., 297, 2021
2DKN
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BU of 2dkn by Molmil
Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831 complexed with NADH
Descriptor: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, 3-alpha-hydroxysteroid dehydrogenase
Authors:Nakamura, S.
Deposit date:2006-04-12
Release date:2006-08-15
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Apo- and Holo-structures of 3{alpha}-Hydroxysteroid Dehydrogenase from Pseudomonas sp. B-0831: LOOP-HELIX TRANSITION INDUCED BY COENZYME BINDING
J.Biol.Chem., 281, 2006

 

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