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PDB: 205 件
1CYQ
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INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX
分子名称: 5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3', INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI, MAGNESIUM ION, ...
著者Galburt, E.A, Chevalier, B, Jurica, M.S, Flick, K.E, Stoddard, B.L.
登録日1999-08-31
公開日1999-11-19
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献A novel endonuclease mechanism directly visualized for I-PpoI.
Nat.Struct.Biol., 6, 1999
3MIS
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I-MsoI re-designed for altered DNA cleavage specificity (-8G)
分子名称: CALCIUM ION, DNA (5'-D(*CP*GP*GP*AP*GP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*CP*CP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*GP*GP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*CP*TP*CP*CP*G)-3'), ...
著者Taylor, G.K, Stoddard, B.L.
登録日2010-04-12
公開日2010-05-19
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Nucleic Acids Res., 38, 2010
4YY5
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Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group P43212
分子名称: dTor_3x33L
著者Hallinan, J.P, Bradley, P, Stoddard, B.L.
登録日2015-03-23
公開日2015-12-16
最終更新日2024-03-06
実験手法X-RAY DIFFRACTION (2.78 Å)
主引用文献Rational design of alpha-helical tandem repeat proteins with closed architectures.
Nature, 528, 2015
1AF5
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GROUP I MOBILE INTRON ENDONUCLEASE
分子名称: I-CREI
著者Heath, P.J, Stephens, K.M, Monnat Junior, R.J, Stoddard, B.L.
登録日1997-03-21
公開日1997-07-23
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献The structure of I-Crel, a group I intron-encoded homing endonuclease.
Nat.Struct.Biol., 4, 1997
3I1C
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BU of 3i1c by Molmil
Crystal Structure of a Novel Engineered Diels-Alderase: DA_20_00_A74I
分子名称: Diisopropyl-fluorophosphatase, GLYCEROL
著者Lambert, A.R, Stoddard, B.L.
登録日2009-06-26
公開日2009-08-18
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
Science, 329, 2010
1IQD
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Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab.
分子名称: HUMAN FACTOR VIII, HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN, HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN
著者Spiegel Jr, P.C, Jacquemin, M, Saint-Remy, J.M, Stoddard, B.L, Pratt, K.P.
登録日2001-07-21
公開日2001-08-15
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII.
Blood, 98, 2001
1G9Y
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HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM
分子名称: 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', CALCIUM ION, ...
著者Chevalier, B, Monnat, R.J, Stoddard, B.L.
登録日2000-11-28
公開日2001-04-02
最終更新日2023-08-09
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001
1EVW
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BU of 1evw by Molmil
L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.
分子名称: DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'), DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3'), DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3'), ...
著者Galburt, E.A, Jurica, M.S, Chevalier, B.S, Erho, D, Stoddard, B.L.
登録日2000-04-20
公開日2000-08-03
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.
J.Mol.Biol., 300, 2000
1G9Z
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LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM
分子名称: 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', ...
著者Chevalier, B, Monnat, R.J, Stoddard, B.L.
登録日2000-11-28
公開日2001-04-02
最終更新日2023-08-09
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001
3E54
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Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA
分子名称: DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3'), ...
著者Nomura, N, Nomura, Y, Sussman, D, Stoddard, B.L.
登録日2008-08-13
公開日2008-12-30
最終更新日2024-05-29
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases
Nucleic Acids Res., 36, 2008
3S1S
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BU of 3s1s by Molmil
Characterization and crystal structure of the type IIG restriction endonuclease BpuSI
分子名称: 1,2-ETHANEDIOL, IODIDE ION, MANGANESE (II) ION, ...
著者Shen, B.W, Xu, D, Chan, S.-H, Zheng, Y, Zhu, Y, Xu, S.-Y, Stoddard, B.L.
登録日2011-05-16
公開日2011-07-13
最終更新日2011-10-19
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.
Nucleic Acids Res., 39, 2011
1OX7
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BU of 1ox7 by Molmil
Crystal structure of yeast cytosine deaminase apo-enzyme: inorganic zinc bound
分子名称: CALCIUM ION, Cytosine deaminase, ZINC ION
著者Ireton, G.C, Black, M.E, Stoddard, B.L.
登録日2003-04-01
公開日2003-08-19
最終更新日2011-07-13
実験手法X-RAY DIFFRACTION (1.43 Å)
主引用文献The 1.14 a crystal structure of yeast Cytosine deaminase. Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
Structure, 11, 2003
3E0L
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BU of 3e0l by Molmil
Computationally Designed Ammelide Deaminase
分子名称: Guanine deaminase, ZINC ION
著者Murphy, P.M, Bolduc, J.M, Gallaher, J.L, Stoddard, B.L, Baker, D.
登録日2008-07-31
公開日2009-03-03
最終更新日2023-08-30
実験手法X-RAY DIFFRACTION (2.37 Å)
主引用文献Alteration of enzyme specificity by computational loop remodeling and design.
Proc.Natl.Acad.Sci.USA, 106, 2009
1CZ0
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BU of 1cz0 by Molmil
INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CATALYTIC METAL ION
分子名称: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'), INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI, SODIUM ION, ...
著者Galburt, E.A, Chevalier, B, Jurica, M.S, Flick, K.E, Stoddard, B.L.
登録日1999-08-31
公開日1999-11-19
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献A novel endonuclease mechanism directly visualized for I-PpoI.
Nat.Struct.Biol., 6, 1999
1B0A
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BU of 1b0a by Molmil
5,10, METHYLENE-TETRAHYDROPHOLATE DEHYDROGENASE/CYCLOHYDROLASE FROM E COLI.
分子名称: PROTEIN (FOLD BIFUNCTIONAL PROTEIN)
著者Shen, B.W, Dyer, D, Huang, J.-Y, D'Ari, L, Rabinowitz, J, Stoddard, B.L.
登録日1998-11-06
公開日1999-06-29
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.56 Å)
主引用文献The crystal structure of a bacterial, bifunctional 5,10 methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
Protein Sci., 8, 1999
4IX0
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BU of 4ix0 by Molmil
Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy
分子名称: NICKEL (II) ION, SULFATE ION, Unnatural Amino Acid Mediated Metalloprotein
著者Mills, J, Bolduc, J, Khare, S, Stoddard, B, Baker, D.
登録日2013-01-24
公開日2013-08-21
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.
J.Am.Chem.Soc., 135, 2013
1IPP
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BU of 1ipp by Molmil
HOMING ENDONUCLEASE/DNA COMPLEX
分子名称: CADMIUM ION, DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'), INTRON-ENCODED ENDONUCLEASE I-PPOI, ...
著者Flick, K.E, Jurica, M.S, Monnat Jr, R.J, Stoddard, B.L.
登録日1998-03-19
公開日1998-09-02
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
4YXY
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Computationally designed left-handed alpha/alpha toroid with 9 repeats; two linked rings of 12 repeats each structure
分子名称: dTor_9x31L
著者Doyle, L, Stoddard, B.L, Bradley, P.
登録日2015-03-23
公開日2015-12-16
最終更新日2024-03-06
実験手法X-RAY DIFFRACTION (3.203 Å)
主引用文献Rational design of alpha-helical tandem repeat proteins with closed architectures.
Nature, 528, 2015
1D7P
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Crystal structure of the c2 domain of human factor viii at 1.5 a resolution at 1.5 A
分子名称: COAGULATION FACTOR VIII PRECURSOR, CYSTEINE, GLYCEROL, ...
著者Pratt, K.P, Shen, B.W, Stoddard, B.L.
登録日1999-10-19
公開日1999-12-01
最終更新日2023-12-13
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Structure of the C2 domain of human factor VIII at 1.5 A resolution.
Nature, 402, 1999
3KO2
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BU of 3ko2 by Molmil
I-MsoI re-designed for altered DNA cleavage specificity (-7C)
分子名称: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', CALCIUM ION, ...
著者Taylor, G.K, Stoddard, B.L.
登録日2009-11-13
公開日2010-05-19
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Nucleic Acids Res., 38, 2010
3MX4
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BU of 3mx4 by Molmil
DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q
分子名称: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3'), Eco29kIR
著者Mak, A.N.S, Lambert, A.R, Stoddard, B.L.
登録日2010-05-06
公開日2010-09-08
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
Structure, 18, 2010
3O6Y
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BU of 3o6y by Molmil
Robust computational design, optimization, and structural characterization of retroaldol enzymes
分子名称: Retro-Aldolase, SULFATE ION
著者Althoff, E.A, Wang, L, Jiang, L, Moody, J, Bolduc, J, Lassila, J.K, Wang, Z.Z, Smith, M, Hari, S, Herschlag, D, Stoddard, B.L, Baker, D.
登録日2010-07-29
公開日2011-06-29
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (2.091 Å)
主引用文献Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
3NXF
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BU of 3nxf by Molmil
Robust computational design, optimization, and structural characterization of retroaldol enzymes
分子名称: Retro-Aldolase, SULFATE ION
著者Althoff, E.A, Jiang, L, Wang, L, Lassila, J.K, Moody, J, Bolduc, J, Wang, Z.Z, Smith, M, Hari, S, Herschlag, D, Stoddard, B.L, Baker, D.
登録日2010-07-13
公開日2011-06-29
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
1QVJ
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structure of NUDT9 complexed with ribose-5-phosphate
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 5-O-phosphono-beta-D-ribofuranose, ADP-ribose pyrophosphatase, ...
著者Shen, B.W, Perraud, A.-L, Scharenberg, A.S, Stoddard, B.L.
登録日2003-08-27
公開日2003-09-16
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (1.91 Å)
主引用文献The crystal structure and mutational analysis of human NUDT9
J.Mol.Biol., 332, 2003
3UD6
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Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design
分子名称: 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE, RETRO-ALDOLASE, SULFATE ION
著者Baker, D, Stoddard, B.L, Althoff, E.A, Wang, L, Jiang, L, Moody, J, Bolduc, J, Lassila, J, Hilvert, D.
登録日2011-10-27
公開日2011-11-23
最終更新日2023-09-13
実験手法X-RAY DIFFRACTION (2.091 Å)
主引用文献Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012

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