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PDB: 319 results

5BCA
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BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES
Descriptor: CALCIUM ION, PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
Authors:Oyama, T, Kusunoki, M, Kishimoto, Y, Takasaki, Y, Nitta, Y.
Deposit date:1999-03-12
Release date:2000-03-15
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.
J.Biochem.(Tokyo), 125, 1999
3VSO
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BU of 3vso by Molmil
Human PPAR gamma ligand binding domain in complex with a gamma selective agonist mekt21
Descriptor: (2R)-2-benzyl-3-[4-propoxy-3-({[4-(pyrimidin-2-yl)benzoyl]amino}methyl)phenyl]propanoic acid, Peroxisome proliferator-activated receptor gamma
Authors:Oyama, T, Waku, T, Ohashi, M, Morikawa, K, Miyachi, H.
Deposit date:2012-04-30
Release date:2013-05-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2 Å)
Cite:Design and synthesis of a series of alpha-benzyl phenylpropanoic acid-type peroxisome proliferator-activated receptor (PPAR) gamma partial agonists with improved aqueous solubility
Bioorg.Med.Chem., 21, 2013
3VSP
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BU of 3vsp by Molmil
Human PPAR gamma ligand binding domain in complex with a gamma selective agonist mekt28
Descriptor: (2R)-2-benzyl-3-[3-({[4-(piperidin-1-yl)benzoyl]amino}methyl)-4-propoxyphenyl]propanoic acid, Peroxisome proliferator-activated receptor gamma
Authors:Oyama, T, Waku, T, Ohashi, M, Morikawa, K, Miyachi, H.
Deposit date:2012-04-30
Release date:2013-05-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Human PPAR gamma ligand binding domain in complex with a gamma selective agonist mekt28
To be Published
3VI8
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BU of 3vi8 by Molmil
Human PPAR alpha ligand binding domain in complex with a synthetic agonist APHM13
Descriptor: (2S)-2-(4-methoxy-3-{[(pyren-1-ylcarbonyl)amino]methyl}benzyl)butanoic acid, Peroxisome proliferator-activated receptor alpha
Authors:Oyama, T, Miyachi, H, Morikawa, K.
Deposit date:2011-09-25
Release date:2012-08-29
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Peroxisome proliferator-activated receptors (PPARs) have multiple binding points that accommodate ligands in various conformations: phenylpropanoic acid-type PPAR ligands bind to PPAR in different conformations, depending on the subtype
J.Med.Chem., 55, 2012
5GHS
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BU of 5ghs by Molmil
DNA replication protein
Descriptor: Putative uncharacterized protein, SULFATE ION, SsDNA-specific exonuclease
Authors:Oyama, T.
Deposit date:2016-06-20
Release date:2016-10-12
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.591 Å)
Cite:Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication.
Nucleic Acids Res., 44, 2016
5GHR
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DNA replication protein
Descriptor: Putative uncharacterized protein, SULFATE ION, SsDNA-specific exonuclease
Authors:Oyama, T.
Deposit date:2016-06-20
Release date:2016-10-12
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (2.509 Å)
Cite:Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication.
Nucleic Acids Res., 44, 2016
5GHT
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BU of 5ght by Molmil
DNA replication protein
Descriptor: SsDNA-specific exonuclease
Authors:Oyama, T.
Deposit date:2016-06-20
Release date:2016-10-12
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.795 Å)
Cite:Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication.
Nucleic Acids Res., 44, 2016
3W0K
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BU of 3w0k by Molmil
Crystal Structure of a glycoside hydrolase
Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Bifunctional endomannanase/endoglucanase
Authors:Oyama, T, Nakamura, H, Morikawa, K, Cann, I.K.O.
Deposit date:2012-10-31
Release date:2013-02-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal structure of a glycoside hydrolase
To be Published
4YT1
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BU of 4yt1 by Molmil
Human PPAR Gamma Ligand Binding Domain in complex with a Gammma Selective Synthetic Partial Agonist MEKT76
Descriptor: N-(benzylsulfonyl)-4-propoxy-3-({[4-(pyrimidin-2-yl)benzoyl]amino}methyl)benzamide, Peroxisome proliferator-activated receptor gamma
Authors:Oyama, T, Ohashi, M, Miyachi, H, Kusunoki, M.
Deposit date:2015-03-17
Release date:2016-03-02
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Peroxisome proliferator-activated receptor gamma (PPAR gamma ) has multiple binding points that accommodate ligands in various conformations: Structurally similar PPAR gamma partial agonists bind to PPAR gamma LBD in different conformations
Bioorg.Med.Chem.Lett., 25, 2015
1J10
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BU of 1j10 by Molmil
beta-amylase from Bacillus cereus var. mycoides in complex with GGX
Descriptor: Beta-amylase, CALCIUM ION, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-xylopyranose, ...
Authors:Oyama, T, Miyake, H, Kusunoki, M, Nitta, Y.
Deposit date:2002-11-25
Release date:2003-06-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents
J.BIOCHEM.(TOKYO), 133, 2003
1J0Z
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Beta-amylase from Bacillus cereus var. mycoides in complex with maltose
Descriptor: Beta-amylase, CALCIUM ION, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ...
Authors:Oyama, T, Miyake, H, Kusunoki, M, Nitta, Y.
Deposit date:2002-11-25
Release date:2003-06-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents
J.BIOCHEM.(TOKYO), 133, 2003
7E15
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BU of 7e15 by Molmil
Protein ternary complex working for DNA replication initiation
Descriptor: DNA polymerase II small subunit, Gins51, SsDNA-specific exonuclease
Authors:Oyama, T, Ishino, Y.
Deposit date:2021-01-30
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome.
Nucleic Acids Res., 50, 2022
1J11
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BU of 1j11 by Molmil
beta-amylase from Bacillus cereus var. mycoides in complex with alpha-EPG
Descriptor: (2R)-oxiran-2-ylmethyl alpha-D-glucopyranoside, Beta-amylase, CALCIUM ION
Authors:Oyama, T, Miyake, H, Kusunoki, M, Nitta, Y.
Deposit date:2002-11-25
Release date:2003-06-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents
J.BIOCHEM.(TOKYO), 133, 2003
1J0Y
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BU of 1j0y by Molmil
Beta-amylase from Bacillus cereus var. mycoides in complex with glucose
Descriptor: Beta-amylase, CALCIUM ION, beta-D-glucopyranose
Authors:Oyama, T, Miyake, H, Kusunoki, M, Nitta, Y.
Deposit date:2002-11-25
Release date:2003-06-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents
J.BIOCHEM.(TOKYO), 133, 2003
1J12
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BU of 1j12 by Molmil
Beta-Amylase from Bacillus cereus var. mycoides in Complex with alpha-EBG
Descriptor: 2-[(2S)-oxiran-2-yl]ethyl alpha-D-glucopyranoside, Beta-amylase, CALCIUM ION
Authors:Oyama, T, Miyake, H, Kusunoki, M, Nitta, Y.
Deposit date:2002-11-25
Release date:2003-06-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents
J.BIOCHEM.(TOKYO), 133, 2003
1IQP
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BU of 1iqp by Molmil
Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
Descriptor: ADENOSINE-5'-DIPHOSPHATE, RFCS
Authors:Oyama, T, Ishino, Y, Cann, I.K.O, Ishino, S, Morikawa, K.
Deposit date:2001-07-24
Release date:2001-09-19
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
Mol.Cell, 8, 2001
3WMH
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BU of 3wmh by Molmil
Human PPAR gamma ligand binding domain in complex with a gammma selective synthetic partial agonist MEKT75
Descriptor: N-(phenylsulfonyl)-4-propoxy-3-({[4-(pyrimidin-2-yl)benzoyl]amino}methyl)benzamide, Peroxisome proliferator-activated receptor gamma
Authors:Oyama, T, Ohashi, M, Miyachi, H, Kusunoki, M.
Deposit date:2013-11-19
Release date:2014-11-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Human PPRR gamma ligand binding domain in complex with a gammma selective synthetic partial agonist MEKT75
TO BE PUBLISHED
7E5F
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BU of 7e5f by Molmil
HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH TIPP703 OBTAINED BY SOAKING
Descriptor: (2S)-2-(4-propoxy-3-{[({4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]phenyl}carbonyl)amino]methyl}benzyl)butanoic acid, Peroxisome proliferator-activated receptor alpha
Authors:Oyama, T, Kamata, S, Ishii, I, Miyachi, H.
Deposit date:2021-02-18
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR) alpha Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method.
Biol.Pharm.Bull., 44, 2021
7E5G
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BU of 7e5g by Molmil
HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH YN4pai OBTAINED BY SOAKING
Descriptor: (2S)-2-[[4-butoxy-3-[(pyren-1-ylcarbonylamino)methyl]phenyl]methyl]butanoic acid, Peroxisome proliferator-activated receptor alpha
Authors:Oyama, T, Kamata, S, Ishii, I, Miyachi, H.
Deposit date:2021-02-18
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR) alpha Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method.
Biol.Pharm.Bull., 44, 2021
7E5I
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BU of 7e5i by Molmil
HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH APHM6 OBTAINED BY SOAKING
Descriptor: (2S)-2-[[3-[[3-fluoranyl-4-(4-fluoranylphenoxy)phenyl]methylcarbamoyl]-4-methoxy-phenyl]methyl]butanoic acid, Peroxisome proliferator-activated receptor alpha
Authors:Oyama, T, Kamata, S, Ishii, I, Miyachi, H.
Deposit date:2021-02-18
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR) alpha Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method.
Biol.Pharm.Bull., 44, 2021
7E5H
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BU of 7e5h by Molmil
HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH APHM6 OBTAINED BY COCRYSTALLIZATION
Descriptor: (2S)-2-[[3-[[3-fluoranyl-4-(4-fluoranylphenoxy)phenyl]methylcarbamoyl]-4-methoxy-phenyl]methyl]butanoic acid, Peroxisome proliferator-activated receptor alpha
Authors:Oyama, T, Kamata, S, Ishii, I, Miyachi, H.
Deposit date:2021-02-18
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR) alpha Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method.
Biol.Pharm.Bull., 44, 2021
7VWF
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BU of 7vwf by Molmil
Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic agonist TIPP204
Descriptor: (2S)-2-{4-butoxy-3-[({[2-fluoro-4-(trifluoromethyl)phenyl]carbonyl}amino)methyl]benzyl}butanoic acid, Peroxisome proliferator-activated receptor delta, heptyl beta-D-glucopyranoside
Authors:Oyama, T, Miyachi, H.
Deposit date:2021-11-10
Release date:2022-02-09
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative.
Acta Crystallogr.,Sect.F, 78, 2022
7VWG
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BU of 7vwg by Molmil
Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic alpha/delta dual agonist JKPL38
Descriptor: (2S)-2-[[4-propoxy-3-[[[4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]methyl]butanoic acid, Peroxisome proliferator-activated receptor delta, heptyl beta-D-glucopyranoside
Authors:Oyama, T, Miyachi, H.
Deposit date:2021-11-10
Release date:2022-02-09
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative.
Acta Crystallogr.,Sect.F, 78, 2022
7VWH
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BU of 7vwh by Molmil
human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic agonist JKPL39
Descriptor: (2S)-2-[[4-hexoxy-3-[[[4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]methyl]butanoic acid, Peroxisome proliferator-activated receptor delta, heptyl beta-D-glucopyranoside
Authors:Oyama, T, Miyachi, H.
Deposit date:2021-11-10
Release date:2022-02-09
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative.
Acta Crystallogr.,Sect.F, 78, 2022
7VWE
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BU of 7vwe by Molmil
Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic partial agonist JK122
Descriptor: 5-[4-butoxy-3-[[[2-fluoranyl-4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]-4,6-dimethyl-pyridine-3-carboxylic acid, Peroxisome proliferator-activated receptor delta, heptyl beta-D-glucopyranoside
Authors:Oyama, T, Miyachi, H.
Deposit date:2021-11-10
Release date:2022-02-09
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3 Å)
Cite:Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative.
Acta Crystallogr.,Sect.F, 78, 2022

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