1U0D
| Y33H Mutant of Homing endonuclease I-CreI | Descriptor: | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3', 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', DNA endonuclease I-CreI | Authors: | Sussman, D, Chadsey, M, Fauce, S, Engel, A, Bruett, A, Monnat, R, Stoddard, B.L, Seligman, L.M. | Deposit date: | 2004-07-13 | Release date: | 2004-11-02 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Isolation and characterization of new homing endonuclease specificities at individual target site positions. J.Mol.Biol., 342, 2004
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1U3E
| DNA binding and cleavage by the HNH homing endonuclease I-HmuI | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 36-MER, ... | Authors: | Shen, B.W, Landthaler, M, Shub, D.A, Stoddard, B.L. | Deposit date: | 2004-07-21 | Release date: | 2004-08-31 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.92 Å) | Cite: | DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI. J.Mol.Biol., 342, 2004
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1UJZ
| Crystal structure of the E7_C/Im7_C complex; a computationally designed interface between the colicin E7 DNase and the Im7 Immunity protein | Descriptor: | Designed Colicin E7 DNase, Designed Colicin E7 immunity protein | Authors: | Kortemme, T, Joachimiak, L.A, Bullock, A.N, Schuler, A.D, Stoddard, B.L, Baker, D. | Deposit date: | 2003-08-13 | Release date: | 2004-04-06 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Computational redesign of protein-protein interaction specificity NAT.STRUCT.MOL.BIOL., 11, 2004
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5IEN
| Structure of CDL2.2, a computationally designed Vitamin-D3 binder | Descriptor: | 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL, CDL2.2, GLYCEROL | Authors: | Stoddard, B.L, Doyle, L.A. | Deposit date: | 2016-02-25 | Release date: | 2017-03-01 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.089 Å) | Cite: | Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Eng.Des.Sel., 31, 2018
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5IEO
| Structure of CDL2.3a, a computationally designed Vitamin-D3 binder | Descriptor: | 1,2-ETHANEDIOL, 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL, CDL2.3a | Authors: | Stoddard, B.L, Doyle, L.A. | Deposit date: | 2016-02-25 | Release date: | 2017-03-01 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.851 Å) | Cite: | Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Eng.Des.Sel., 31, 2018
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5IEP
| Structure of CDL2.3b, a computationally designed Vitamin-D3 binder | Descriptor: | 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL, CDL2.3b | Authors: | Stoddard, B.L, Doyle, L.A. | Deposit date: | 2016-02-25 | Release date: | 2017-03-01 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.893 Å) | Cite: | Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Eng.Des.Sel., 31, 2018
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4VGC
| GAMMA-CHYMOTRYPSIN D-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX | Descriptor: | D-1-NAPHTHYL-2-ACETAMIDO-ETHANE BORONIC ACID, GAMMA CHYMOTRYPSIN, SULFATE ION | Authors: | Stoll, V.S, Eger, B.T, Hynes, R.C, Martichonok, V, Jones, J.B, Pai, E.F. | Deposit date: | 1997-05-01 | Release date: | 1997-11-12 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry, 37, 1998
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8GLT
| Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 | Descriptor: | C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model, C3-comp_O32-15 | Authors: | Redler, R.L, Ennist, N.M, Wang, S, Baker, D, Ekiert, D.C, Bhabha, G. | Deposit date: | 2023-03-23 | Release date: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (6.5 Å) | Cite: | De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs To Be Published
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1A74
| I-PPOL HOMING ENDONUCLEASE/DNA COMPLEX | Descriptor: | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*A P*GP*TP*CP*A)-3'), INTRON-ENCODED ENDONUCLEASE I-PPOI, ZINC ION | Authors: | Jurica, B.L, Flick, K.E, Monnat Junior, R.J, Stoddard, M.S. | Deposit date: | 1998-03-19 | Release date: | 1998-06-22 | 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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3UVF
| Expanding LAGALIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, Intron-encoded DNA endonuclease I-HjeMI, ... | Authors: | Jacoby, K, Metzger, M, Shen, B, Jarjour, J, Stoddard, B, Scharenberg, A. | Deposit date: | 2011-11-29 | Release date: | 2012-02-29 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space. Nucleic Acids Res., 40, 2012
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1VGC
| GAMMA-CHYMOTRYPSIN L-PARA-CHLORO-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX | Descriptor: | GAMMA CHYMOTRYPSIN, L-1-(4-CHLOROPHENYL)-2-(ACETAMIDO)ETHANE BORONIC ACID, SULFATE ION | Authors: | Stoll, V.S, Eger, B.T, Hynes, R.C, Martichonok, V, Jones, J.B, Pai, E.F. | Deposit date: | 1997-05-01 | Release date: | 1997-11-12 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry, 37, 1998
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2VGC
| GAMMA-CHYMOTRYPSIN D-PARA-CHLORO-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX | Descriptor: | D-1-(4-CHLOROPHENYL)-2-(ACETAMIDO)ETHANE BORONIC ACID, GAMMA CHYMOTRYPSIN, SULFATE ION | Authors: | Stoll, V.S, Eger, B.T, Hynes, R.C, Martichonok, V, Jones, J.B, Pai, E.F. | Deposit date: | 1997-05-01 | Release date: | 1997-11-12 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry, 37, 1998
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3VGC
| GAMMA-CHYMOTRYPSIN L-NAPHTHYL-1-ACETAMIDO BORONIC ACID ACID INHIBITOR COMPLEX | Descriptor: | GAMMA CHYMOTRYPSIN, L-1-NAPHTHYL-2-ACETAMIDO-ETHANE BORONIC ACID, SULFATE ION | Authors: | Stoll, V.S, Eger, B.T, Hynes, R.C, Martichonok, V, Jones, J.B, Pai, E.F. | Deposit date: | 1997-05-01 | Release date: | 1997-11-12 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (1.67 Å) | Cite: | Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry, 37, 1998
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2GJH
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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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4IWW
| Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy | Descriptor: | COBALT (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 (2.3 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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2I3P
| K28R mutant of Homing Endonuclease I-CreI | Descriptor: | 5'-D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP*TP*TP*TP*CP*G)-3', CALCIUM ION, ... | Authors: | Sussman, D, Rosen, L. | Deposit date: | 2006-08-20 | Release date: | 2006-09-05 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucleic Acids Res., 34, 2006
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2I3Q
| Q44V mutant of Homing Endonuclease I-CreI | Descriptor: | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*AP*CP*TP*CP*AP*CP*GP*TP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP*GP*TP*TP*TP*CP*G)-3', CALCIUM ION, ... | Authors: | Rosen, L, Sussman, D. | Deposit date: | 2006-08-20 | Release date: | 2006-09-05 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucleic Acids Res., 34, 2006
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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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5CW9
| Crystal structure of De novo designed ferredoxin-ferredoxin domain insertion protein | Descriptor: | De novo designed ferredoxin-ferredoxin domain insertion protein | Authors: | DiMaio, F, King, I.C, Gleixner, J, Doyle, L, Stoddard, B, Baker, D. | Deposit date: | 2015-07-28 | Release date: | 2015-09-23 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (3.108 Å) | Cite: | Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife, 4, 2015
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5E63
| K262A mutant of I-SmaMI | Descriptor: | 2-(2-METHOXYETHOXY)ETHANOL, 2-METHOXYETHANOL, DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3'), ... | Authors: | Shen, B, Stoddard, B. | Deposit date: | 2015-10-09 | Release date: | 2016-01-13 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease. J.Mol.Biol., 428, 2016
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5E67
| K103A/K262A double mutant of I-SmaMI | Descriptor: | 2-(2-METHOXYETHOXY)ETHANOL, 2-METHOXYETHANOL, DNA bottom strand, ... | Authors: | Shen, B.W, Stoddard, B. | Deposit date: | 2015-10-09 | Release date: | 2016-01-13 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease. J.Mol.Biol., 428, 2016
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4OYD
| Crystal structure of a computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein | Descriptor: | 1,2-ETHANEDIOL, Apoptosis regulator BHRF1, Computationally designed Inhibitor | Authors: | Shen, B, Procko, E, Baker, D, Stoddard, B. | Deposit date: | 2014-02-11 | Release date: | 2014-07-09 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells. Cell, 157, 2014
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7T8K
| BrxR from Acinetobacter BREX type I phage restriction system bound to DNA | Descriptor: | 1,2-ETHANEDIOL, BrxR, CHLORIDE ION, ... | Authors: | Doyle, L, Kaiser, B, Stoddard, B. | Deposit date: | 2021-12-16 | Release date: | 2022-05-18 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Nucleic Acids Res., 50, 2022
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7T8L
| BrxR from Acinetobacter BREX type I phage restriction system | Descriptor: | 1,2-ETHANEDIOL, BrxR, CHLORIDE ION | Authors: | Doyle, L, Kaiser, B, Stoddard, B. | Deposit date: | 2021-12-16 | Release date: | 2022-05-18 | Last modified: | 2022-06-01 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Nucleic Acids Res., 50, 2022
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