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1F2D
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BU of 1f2d by Molmil
1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
Descriptor: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE, PYRIDOXAL-5'-PHOSPHATE, SULFATE ION
Authors:Yao, M, Ose, T, Sugimoto, H, Horiuchi, A, Nakagawa, A, Yokoi, D, Murakami, T, Honma, M, Wakatsuki, S, Tanaka, I.
Deposit date:2000-05-24
Release date:2000-12-20
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus.
J.Biol.Chem., 275, 2000
1IZ6
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BU of 1iz6 by Molmil
Crystal Structure of Translation Initiation Factor 5A from Pyrococcus Horikoshii
Descriptor: Initiation Factor 5A
Authors:Yao, M, Ohsawa, A, Kikukawa, S, Tanaka, I, Kimura, M.
Deposit date:2002-09-25
Release date:2003-01-28
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal Structure of Hyperthermophilic Archaeal Initiation Factor 5A: A Homologue of Eukaryotic Initiation Factor 5A (eIF-5A)
J.BIOCHEM.(TOKYO), 133, 2003
1WLS
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BU of 1wls by Molmil
Crystal structure of L-asparaginase I homologue protein from Pyrococcus horikoshii
Descriptor: L-asparaginase
Authors:Yao, M, Morita, H, Yasutake, Y, Tanaka, I.
Deposit date:2004-06-29
Release date:2005-03-15
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.16 Å)
Cite:Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.
Acta Crystallogr.,Sect.D, 61, 2005
2ZQ0
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BU of 2zq0 by Molmil
Crystal structure of SusB complexed with acarbose
Descriptor: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, Alpha-glucosidase (Alpha-glucosidase SusB), CALCIUM ION
Authors:Yao, M, Tanaka, I, Kitamura, M.
Deposit date:2008-07-31
Release date:2008-10-28
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.
J.Biol.Chem., 283, 2008
1V7L
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BU of 1v7l by Molmil
Structure of 3-isopropylmalate isomerase small subunit from Pyrococcus horikoshii
Descriptor: 3-isopropylmalate dehydratase small subunit
Authors:Yao, M, Kirita, T, Sakai, N, Tanaka, I.
Deposit date:2003-12-18
Release date:2004-11-16
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Crystal Structure of the Pyrococcus horikoshii Isopropylmalate Isomerase Small Subunit Provides Insight into the Dual Substrate Specificity of the Enzyme
J.Mol.Biol., 344, 2004
1VGJ
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BU of 1vgj by Molmil
Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii
Descriptor: Hypothetical protein PH0099
Authors:Yao, M, Morita, H, Okada, A, Tanaka, I.
Deposit date:2004-04-27
Release date:2005-06-07
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:The structure of Pyrococcus horikoshii 2'-5' RNA ligase at 1.94 A resolution reveals a possible open form with a wider active-site cleft
ACTA CRYSTALLOGR.,SECT.F, 62, 2006
1EL1
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BU of 1el1 by Molmil
X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (HOLO-TYPE)
Descriptor: CALCIUM ION, LYSOZYME C
Authors:Koshiba, T, Yao, M, Tanaka, I, Nitta, K.
Deposit date:2000-03-13
Release date:2001-03-13
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Calcium Induced Conformational Changes of Canine Milk Lysozyme Revealed by Structural and Thermodynamical Evidences
To be Published
1OCO
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BU of 1oco by Molmil
BOVINE HEART CYTOCHROME C OXIDASE IN CARBON MONOXIDE-BOUND STATE
Descriptor: CARBON MONOXIDE, COPPER (II) ION, CYTOCHROME C OXIDASE, ...
Authors:Tsukihara, T, Yao, M.
Deposit date:1998-07-09
Release date:1999-07-22
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.
Science, 280, 1998
4P1Y
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BU of 4p1y by Molmil
Crystal structure of staphylococcal gamma-hemolysin prepore
Descriptor: Gamma-hemolysin component A, Gamma-hemolysin component B
Authors:Yamashita, D, Tanaka, Y, Tanaka, I, Yao, M.
Deposit date:2014-02-28
Release date:2014-10-01
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.992 Å)
Cite:Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
Nat Commun, 5, 2014
4P1X
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BU of 4p1x by Molmil
Crystal structure of staphylococcal LUK prepore
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Gamma-hemolysin component B, Gamma-hemolysin component C
Authors:Yamashita, D, Tanaka, Y, Tanaka, I, Yao, M.
Deposit date:2014-02-28
Release date:2014-10-01
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
Nat Commun, 5, 2014
4WLC
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BU of 4wlc by Molmil
Structure of dextran glucosidase with glucose
Descriptor: CALCIUM ION, GLYCEROL, Glucan 1,6-alpha-glucosidase, ...
Authors:Kobayashi, M, Kato, K, Yao, M.
Deposit date:2014-10-07
Release date:2015-08-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.402 Å)
Cite:Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase
Febs Lett., 589, 2015
4P24
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BU of 4p24 by Molmil
pore forming toxin
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Alpha-hemolysin
Authors:Sugawara, T, Yamashita, D, Tanaka, Y, Tanaka, I, Yao, M.
Deposit date:2014-03-01
Release date:2015-03-11
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structural basis for pore-forming mechanism of staphylococcal alpha-hemolysin.
Toxicon, 108, 2015
4V60
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BU of 4v60 by Molmil
The structure of rat liver vault at 3.5 angstrom resolution
Descriptor: Major vault protein
Authors:Kato, K, Zhou, Y, Tanaka, H, Yao, M, Yamashita, E, Yoshimura, M, Tsukihara, T.
Deposit date:2008-10-24
Release date:2014-07-09
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:The structure of rat liver vault at 3.5 angstrom resolution
Science, 323, 2009
5IP3
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BU of 5ip3 by Molmil
Tomato spotted wilt tospovirus nucleocapsid protein-ssDNA complex
Descriptor: DNA (5'-D(P*TP*TP*TP*TP*T)-3'), DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3'), DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3'), ...
Authors:Komoda, K, Narita, M, Yamashita, K, Tanaka, I, Yao, M.
Deposit date:2016-03-09
Release date:2017-03-22
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3 Å)
Cite:Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
J. Virol., 91, 2017
5IP2
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BU of 5ip2 by Molmil
Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex
Descriptor: Nucleoprotein, RNA (5'-D(P*UP*UP*U)-3'), RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Authors:Komoda, K, Narita, M, Yamashita, K, Tanaka, I, Yao, M.
Deposit date:2016-03-09
Release date:2017-03-22
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
J. Virol., 91, 2017
4WJ3
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BU of 4wj3 by Molmil
Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa
Descriptor: 76mer-tRNA, Aspartate--tRNA(Asp/Asn) ligase, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, ...
Authors:Suzuki, T, Nakamura, A, Kato, K, Tanaka, I, Yao, M.
Deposit date:2014-09-29
Release date:2014-12-31
Last modified:2020-02-05
Method:X-RAY DIFFRACTION (3.705 Å)
Cite:Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Proc.Natl.Acad.Sci.USA, 112, 2015
8IN4
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BU of 8in4 by Molmil
Eisenia hydrolysis-enhancing protein from Aplysia kurodai
Descriptor: 25 kDa polyphenol-binding protein, ACETYL GROUP, GLYCEROL
Authors:Sun, X.M, Ye, Y.X, Kato, K, Yu, J, Yao, M.
Deposit date:2023-03-08
Release date:2023-11-15
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.
Elife, 12, 2023
8IN1
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BU of 8in1 by Molmil
beta-glucosidase protein from Aplysia kurodai
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-Glucosidase, alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Sun, X.M, Ye, Y.X, Kato, K, Yu, J, Yao, M.
Deposit date:2023-03-08
Release date:2023-11-15
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.
Elife, 12, 2023
8IN3
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BU of 8in3 by Molmil
Eisenia hydrolysis-enhancing protein from Aplysia kurodai
Descriptor: 25 kDa polyphenol-binding protein, GLYCEROL
Authors:Sun, X.M, Ye, Y.X, Kato, K, Yu, J, Yao, M.
Deposit date:2023-03-08
Release date:2023-11-15
Method:X-RAY DIFFRACTION (1.15 Å)
Cite:Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.
Elife, 12, 2023
8IN6
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BU of 8in6 by Molmil
Eisenia hydrolysis-enhancing protein from Aplysia kurodai complex with tannic acid
Descriptor: 25 kDa polyphenol-binding protein, BETA-1,2,3,4,6-PENTA-O-GALLOYL-D-GLUCOPYRANOSE
Authors:Sun, X.M, Ye, Y.X, Kato, K, Yu, J, Yao, M.
Deposit date:2023-03-08
Release date:2023-11-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.
Elife, 12, 2023
3VO9
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BU of 3vo9 by Molmil
Staphylococcus aureus FtsZ apo-form (SeMet)
Descriptor: Cell division protein FtsZ
Authors:Matsui, T, Yamane, J, Mogi, N, Yao, M, Tanaka, I.
Deposit date:2012-01-20
Release date:2012-08-29
Last modified:2013-08-14
Method:X-RAY DIFFRACTION (2.706 Å)
Cite:Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus
Acta Crystallogr.,Sect.D, 68, 2012
8YIE
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BU of 8yie by Molmil
Crystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarbose
Descriptor: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, Alpha-glucosidase
Authors:Saburi, W, Tagami, T, Yu, J, Ose, T, Yao, M, Mori, H.
Deposit date:2024-02-29
Release date:2024-07-03
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Molecular mechanism for the substrate specificity of Arthrobacter globiformis M6 alpha-glucosidase CmmB, belonging to glycoside hydrolase family 13 subfamily 30
Food Biosci, 61, 2024
8YIF
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BU of 8yif by Molmil
Crystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarviosin
Descriptor: Acarviosin, Alpha-glucosidase
Authors:Saburi, W, Tagami, T, Yu, J, Ose, T, Yao, M, Mori, H.
Deposit date:2024-02-29
Release date:2024-07-03
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Molecular mechanism for the substrate specificity of Arthrobacter globiformis M6 alpha-glucosidase CmmB, belonging to glycoside hydrolase family 13 subfamily 30
Food Biosci, 61, 2024
3VOA
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BU of 3voa by Molmil
Staphylococcus aureus FtsZ 12-316 GDP-form
Descriptor: CALCIUM ION, Cell division protein FtsZ, GUANOSINE-5'-DIPHOSPHATE
Authors:Yamane, J, Matsui, T, Mogi, N, Yao, M, Tanaka, I.
Deposit date:2012-01-20
Release date:2012-08-29
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus
Acta Crystallogr.,Sect.D, 68, 2012
3VZR
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BU of 3vzr by Molmil
Crystal structure of T173S mutant of PhaB from Ralstonia eutropha
Descriptor: Acetoacetyl-CoA reductase
Authors:Ikeda, K, Tanaka, Y, Tanaka, I, Yao, M.
Deposit date:2012-10-15
Release date:2013-08-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.901 Å)
Cite:Directed evolution and structural analysis of NADPH-dependent Acetoacetyl Coenzyme A (Acetoacetyl-CoA) reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics
Appl.Environ.Microbiol., 79, 2013

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PDB entries from 2024-09-25

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