1CYQ
 
 | | INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX | | Descriptor: | 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, ... | | Authors: | Galburt, E.A, Chevalier, B, Jurica, M.S, Flick, K.E, Stoddard, B.L. | | Deposit date: | 1999-08-31 | | Release date: | 1999-11-19 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | A novel endonuclease mechanism directly visualized for I-PpoI.
Nat.Struct.Biol., 6, 1999
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3MIS
 | | I-MsoI re-designed for altered DNA cleavage specificity (-8G) | | Descriptor: | 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'), ... | | Authors: | Taylor, G.K, Stoddard, B.L. | | Deposit date: | 2010-04-12 | | Release date: | 2010-05-19 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Nucleic Acids Res., 38, 2010
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4YY5
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1AF5
 | | GROUP I MOBILE INTRON ENDONUCLEASE | | Descriptor: | I-CREI | | Authors: | Heath, P.J, Stephens, K.M, Monnat Junior, R.J, Stoddard, B.L. | | Deposit date: | 1997-03-21 | | Release date: | 1997-07-23 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | The structure of I-Crel, a group I intron-encoded homing endonuclease.
Nat.Struct.Biol., 4, 1997
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3I1C
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1IQD
 | | Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab. | | Descriptor: | HUMAN FACTOR VIII, HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN, HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN | | Authors: | Spiegel Jr, P.C, Jacquemin, M, Saint-Remy, J.M, Stoddard, B.L, Pratt, K.P. | | Deposit date: | 2001-07-21 | | Release date: | 2001-08-15 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 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
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1G9Y
 | | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | | Descriptor: | 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, ... | | Authors: | Chevalier, B, Monnat, R.J, Stoddard, B.L. | | Deposit date: | 2000-11-28 | | Release date: | 2001-04-02 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001
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1EVW
 | | L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA. | | Descriptor: | 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'), ... | | Authors: | Galburt, E.A, Jurica, M.S, Chevalier, B.S, Erho, D, Stoddard, B.L. | | Deposit date: | 2000-04-20 | | Release date: | 2000-08-03 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | 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
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1G9Z
 | | LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM | | Descriptor: | 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', ... | | Authors: | Chevalier, B, Monnat, R.J, Stoddard, B.L. | | Deposit date: | 2000-11-28 | | Release date: | 2001-04-02 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001
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3E54
 | | Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA | | Descriptor: | 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'), ... | | Authors: | Nomura, N, Nomura, Y, Sussman, D, Stoddard, B.L. | | Deposit date: | 2008-08-13 | | Release date: | 2008-12-30 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | 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
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3S1S
 | | Characterization and crystal structure of the type IIG restriction endonuclease BpuSI | | Descriptor: | 1,2-ETHANEDIOL, IODIDE ION, MANGANESE (II) ION, ... | | Authors: | Shen, B.W, Xu, D, Chan, S.-H, Zheng, Y, Zhu, Y, Xu, S.-Y, Stoddard, B.L. | | Deposit date: | 2011-05-16 | | Release date: | 2011-07-13 | | Last modified: | 2011-10-19 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.
Nucleic Acids Res., 39, 2011
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1OX7
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3E0L
 | | Computationally Designed Ammelide Deaminase | | Descriptor: | Guanine deaminase, ZINC ION | | Authors: | Murphy, P.M, Bolduc, J.M, Gallaher, J.L, Stoddard, B.L, Baker, D. | | Deposit date: | 2008-07-31 | | Release date: | 2009-03-03 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.37 Å) | | Cite: | Alteration of enzyme specificity by computational loop remodeling and design.
Proc.Natl.Acad.Sci.USA, 106, 2009
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1CZ0
 | | INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CATALYTIC METAL ION | | Descriptor: | 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, ... | | Authors: | Galburt, E.A, Chevalier, B, Jurica, M.S, Flick, K.E, Stoddard, B.L. | | Deposit date: | 1999-08-31 | | Release date: | 1999-11-19 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | A novel endonuclease mechanism directly visualized for I-PpoI.
Nat.Struct.Biol., 6, 1999
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1B0A
 | | 5,10, METHYLENE-TETRAHYDROPHOLATE DEHYDROGENASE/CYCLOHYDROLASE FROM E COLI. | | Descriptor: | PROTEIN (FOLD BIFUNCTIONAL PROTEIN) | | Authors: | Shen, B.W, Dyer, D, Huang, J.-Y, D'Ari, L, Rabinowitz, J, Stoddard, B.L. | | Deposit date: | 1998-11-06 | | Release date: | 1999-06-29 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | The crystal structure of a bacterial, bifunctional 5,10 methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
Protein Sci., 8, 1999
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4IX0
 | | Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy | | Descriptor: | NICKEL (II) ION, SULFATE ION, Unnatural Amino Acid Mediated Metalloprotein | | Authors: | Mills, J, Bolduc, J, Khare, S, Stoddard, B, Baker, D. | | Deposit date: | 2013-01-24 | | Release date: | 2013-08-21 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.
J.Am.Chem.Soc., 135, 2013
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1IPP
 | | HOMING ENDONUCLEASE/DNA COMPLEX | | Descriptor: | 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, ... | | Authors: | Flick, K.E, Jurica, M.S, Monnat Jr, R.J, Stoddard, B.L. | | Deposit date: | 1998-03-19 | | Release date: | 1998-09-02 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
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4YXY
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1D7P
 | | Crystal structure of the c2 domain of human factor viii at 1.5 a resolution at 1.5 A | | Descriptor: | COAGULATION FACTOR VIII PRECURSOR, CYSTEINE, GLYCEROL, ... | | Authors: | Pratt, K.P, Shen, B.W, Stoddard, B.L. | | Deposit date: | 1999-10-19 | | Release date: | 1999-12-01 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure of the C2 domain of human factor VIII at 1.5 A resolution.
Nature, 402, 1999
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3KO2
 | | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | | Descriptor: | 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, ... | | Authors: | Taylor, G.K, Stoddard, B.L. | | Deposit date: | 2009-11-13 | | Release date: | 2010-05-19 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Nucleic Acids Res., 38, 2010
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3MX4
 | | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | | Descriptor: | 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 | | Authors: | Mak, A.N.S, Lambert, A.R, Stoddard, B.L. | | Deposit date: | 2010-05-06 | | Release date: | 2010-09-08 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
Structure, 18, 2010
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3O6Y
 | | Robust computational design, optimization, and structural characterization of retroaldol enzymes | | Descriptor: | Retro-Aldolase, SULFATE ION | | Authors: | 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. | | Deposit date: | 2010-07-29 | | Release date: | 2011-06-29 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.091 Å) | | Cite: | 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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3NXF
 | | Robust computational design, optimization, and structural characterization of retroaldol enzymes | | Descriptor: | Retro-Aldolase, SULFATE ION | | Authors: | 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. | | Deposit date: | 2010-07-13 | | Release date: | 2011-06-29 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | 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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1QVJ
 | | structure of NUDT9 complexed with ribose-5-phosphate | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 5-O-phosphono-beta-D-ribofuranose, ADP-ribose pyrophosphatase, ... | | Authors: | Shen, B.W, Perraud, A.-L, Scharenberg, A.S, Stoddard, B.L. | | Deposit date: | 2003-08-27 | | Release date: | 2003-09-16 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | The crystal structure and mutational analysis of human NUDT9
J.Mol.Biol., 332, 2003
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3UD6
 | | Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design | | Descriptor: | 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE, RETRO-ALDOLASE, SULFATE ION | | Authors: | Baker, D, Stoddard, B.L, Althoff, E.A, Wang, L, Jiang, L, Moody, J, Bolduc, J, Lassila, J, Hilvert, D. | | Deposit date: | 2011-10-27 | | Release date: | 2011-11-23 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.091 Å) | | Cite: | 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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