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5Z76
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BU of 5z76 by Molmil
Artificial L-threonine 3-dehydrogenase designed by full consensus design
Descriptor: Artificial L-threonine 3-dehydrogenase
Authors:Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S.
Deposit date:2018-01-27
Release date:2018-08-22
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
5Z75
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BU of 5z75 by Molmil
Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.
Descriptor: Artificial L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, NONAETHYLENE GLYCOL, ...
Authors:Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S.
Deposit date:2018-01-27
Release date:2018-08-22
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
4Y7P
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BU of 4y7p by Molmil
Structure of alkaline D-peptidase from Bacillus cereus
Descriptor: Alkaline D-peptidase, THIOCYANATE ION
Authors:Nakano, S, Okazaki, S, Ishitsubo, E, Kawahara, N, Komeda, H, Tokiwa, H, Asano, Y.
Deposit date:2015-02-15
Release date:2015-10-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B
Sci Rep, 5, 2015
3WMW
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BU of 3wmw by Molmil
GalE-like L-Threonine dehydrogenase from Cupriavidus necator (apo form)
Descriptor: CALCIUM ION, NAD dependent epimerase/dehydratase
Authors:Nakano, S, Okazaki, S, Tokiwa, H, Asano, Y.
Deposit date:2013-11-29
Release date:2014-02-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase
J.Biol.Chem., 289, 2014
3WMX
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BU of 3wmx by Molmil
GalE-like L-Threonine dehydrogenase from Cupriavidus necator (holo form)
Descriptor: NAD dependent epimerase/dehydratase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, THREONINE
Authors:Nakano, S, Okazaki, S, Tokiwa, H, Asano, Y.
Deposit date:2013-11-29
Release date:2014-02-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase
J.Biol.Chem., 289, 2014
4YJF
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BU of 4yjf by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form)
Descriptor: (1S)-1-phenylethanamine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ...
Authors:Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
Deposit date:2015-03-03
Release date:2016-04-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of DAAO variant
To Be Published
3WWO
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BU of 3wwo by Molmil
S-selective hydroxynitrile lyase from Baliospermum montanum (apo1)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, (S)-hydroxynitrile lyase, CALCIUM ION
Authors:Nakano, S, Dadashipour, M, Asano, Y.
Deposit date:2014-06-23
Release date:2014-10-22
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
Biochim.Biophys.Acta, 1844, 2014
4YJH
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BU of 4yjh by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form)
Descriptor: (2R)-2-phenylpyrrolidine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ...
Authors:Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
Deposit date:2015-03-03
Release date:2016-04-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Crystal structure of DAAO variant
To Be Published
4YJG
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BU of 4yjg by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)
Descriptor: (2R)-4-phenylbutan-2-amine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ...
Authors:Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
Deposit date:2015-03-03
Release date:2016-04-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structure of DAAO variant
To Be Published
3WWP
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BU of 3wwp by Molmil
S-selective hydroxynitrile lyase from Baliospermum montanum (apo2)
Descriptor: (S)-hydroxynitrile lyase, 1,2-ETHANEDIOL, CHLORIDE ION, ...
Authors:Nakano, S, Dadashipour, M, Asano, Y.
Deposit date:2014-06-23
Release date:2014-10-22
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
Biochim.Biophys.Acta, 1844, 2014
4YJD
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BU of 4yjd by Molmil
Crystal structure of DAAO(Y228L/R283G) variant (apo form)
Descriptor: D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION
Authors:Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y.
Deposit date:2015-03-03
Release date:2016-04-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of DAAO variant
To Be Published
7C4N
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BU of 7c4n by Molmil
Ancestral L-amino acid oxidase (AncLAAO-N5) L-Phe binding form
Descriptor: Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, PHENYLALANINE
Authors:Nakano, S, Minamino, Y, Karasuda, H, Ito, S.
Deposit date:2020-05-18
Release date:2020-12-02
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
7C4L
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BU of 7c4l by Molmil
Anncestral L-amino acid oxidase (AncLAAO-N5) L-Gln binding form
Descriptor: FLAVIN-ADENINE DINUCLEOTIDE, GLUTAMINE, L-amino acid oxidase
Authors:Nakano, S, Minamino, Y, Karasuda, H, Ito, S.
Deposit date:2020-05-18
Release date:2020-12-02
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
7C4M
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BU of 7c4m by Molmil
Ancestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form
Descriptor: Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, TRYPTOPHAN
Authors:Nakano, S, Minamino, Y, Karasuda, H, Ito, S.
Deposit date:2020-05-18
Release date:2020-12-02
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
7C4K
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BU of 7c4k by Molmil
Ancestral L-amino acid oxidase (AncLAAO-N5) ligand free form
Descriptor: Ancestral L-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE
Authors:Nakano, S, Minamino, Y, Karasuda, H, Ito, S.
Deposit date:2020-05-18
Release date:2020-12-02
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Commun Chem, 3, 2020
3VLG
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BU of 3vlg by Molmil
Crystal structure of the W150A mutant LOX-1 CTLD showing impaired OxLDL binding
Descriptor: Oxidized low-density lipoprotein receptor 1
Authors:Nakano, S, Sugihara, M, Yamada, R, Katayanagi, K, Tate, S.
Deposit date:2011-12-01
Release date:2012-04-18
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural implication for the impaired binding of W150A mutant LOX-1 to oxidized low density lipoprotein, OxLDL
Biochim.Biophys.Acta, 1824, 2012
3VKR
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BU of 3vkr by Molmil
Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with high X-ray dose
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, NITRITE ION, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-11-20
Release date:2012-04-25
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy
Proteins, 80, 2012
3VLZ
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BU of 3vlz by Molmil
Assimilatory nitrite reductase (Nii3) - N226K mutant - SO3 full complex from tobacco leaf
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, Nitrite reductase, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-12-05
Release date:2012-09-26
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Chem.Biodivers., 9, 2012
3VKQ
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BU of 3vkq by Molmil
Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with middle X-ray dose
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, NITRITE ION, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-11-20
Release date:2012-04-25
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy
Proteins, 80, 2012
3VKS
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BU of 3vks by Molmil
Assimilatory nitrite reductase (Nii3) - NO complex from tobbaco leaf
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, NITRIC OXIDE, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-11-20
Release date:2012-04-25
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy
Proteins, 80, 2012
3VLY
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BU of 3vly by Molmil
Assimilatory nitrite reductase (Nii3) - N226K mutant - SO3 partial complex from tobacco leaf
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, Nitrite reductase, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-12-05
Release date:2012-09-26
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Chem.Biodivers., 9, 2012
3VM0
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BU of 3vm0 by Molmil
Assimilatory nitrite reductase (Nii3) - N226K mutant - NO2 complex from tobacco leaf
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, NITRITE ION, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-12-05
Release date:2012-09-26
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.695 Å)
Cite:X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Chem.Biodivers., 9, 2012
3VM1
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BU of 3vm1 by Molmil
assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 complex from tobacco leaf
Descriptor: BICARBONATE ION, CHLORIDE ION, IRON/SULFUR CLUSTER, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-12-05
Release date:2012-09-26
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Chem.Biodivers., 9, 2012
3VLX
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BU of 3vlx by Molmil
Assimilatory nitrite reductase (Nii3) - N226K mutant - ligand free form from tobacco leaf
Descriptor: CHLORIDE ION, IRON/SULFUR CLUSTER, Nitrite reductase, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-12-05
Release date:2012-09-26
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Chem.Biodivers., 9, 2012
3VKT
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BU of 3vkt by Molmil
Assimilatory nitrite reductase (Nii3) - NH2OH complex from tobbaco leaf
Descriptor: CHLORIDE ION, HYDROXYAMINE, IRON/SULFUR CLUSTER, ...
Authors:Nakano, S, Takahashi, M, Sakamoto, A, Morikawa, H, Katayanagi, K.
Deposit date:2011-11-20
Release date:2012-04-25
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy
Proteins, 80, 2012

 

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