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: | 2024-11-13 | | 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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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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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 | | Last modified: | 2024-07-10 | | Method: | ELECTRON MICROSCOPY (6.5 Å) | | Cite: | De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 20, 2024
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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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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: | 2024-11-27 | | 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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5V0Q
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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: | 2024-12-25 | | 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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7RKC
 | | Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633 | | Descriptor: | ACETATE ION, D_3_633 | | Authors: | Kennedy, M.A, Stoddard, B.L, Hicks, D.R, Bera, A.K. | | Deposit date: | 2021-07-22 | | Release date: | 2022-05-18 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | De novo design of protein homodimers containing tunable symmetric protein pockets.
Proc.Natl.Acad.Sci.USA, 119, 2022
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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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5E5S
 | | I-SmaMI K103A mutant | | Descriptor: | 2-(2-METHOXYETHOXY)ETHANOL, Bottom strand DNA, DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3'), ... | | Authors: | Shen, B.W. | | Deposit date: | 2015-10-09 | | Release date: | 2016-01-13 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.29 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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5E5P
 | | Wild type I-SmaMI in the space group of C121 | | Descriptor: | 1,2-ETHANEDIOL, 2-(2-METHOXYETHOXY)ETHANOL, I-SmaMI LAGLIDADG meganuclease | | Authors: | Shen, B.W. | | Deposit date: | 2015-10-09 | | Release date: | 2016-01-13 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.65 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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5E5O
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2GJH
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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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3FD2
 | | Crystal structure of mMsoI/DNA complex with calcium | | Descriptor: | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', CALCIUM ION, ... | | Authors: | Li, H, Monnat, R.J. | | Deposit date: | 2008-11-24 | | Release date: | 2009-06-30 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.69 Å) | | Cite: | Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.
Nucleic Acids Res., 37, 2009
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4KYZ
 | | Three-dimensional structure of triclinic form of de novo design insertion domain, Northeast Structural Genomics Consortium (NESG) Target OR327 | | Descriptor: | Designed protein OR327 | | Authors: | Kuzin, A, Su, M, Seetharaman, J, Maglaqui, M, Xiao, R, Lee, D, Gleixner, J, Baker, D, Everett, J.K, Acton, T.B, Kornhaber, G, Montelione, G.T, Hunt, J.F, Tong, L, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2013-05-29 | | Release date: | 2013-07-24 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.492 Å) | | Cite: | Precise assembly of complex beta sheet topologies from de novo designed building blocks.
Elife, 4, 2015
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4J9T
 | | Crystal structure of a putative, de novo designed unnatural amino acid dependent metalloprotein, northeast structural genomics consortium target OR61 | | Descriptor: | ARSENIC, GLYCEROL, designed unnatural amino acid dependent metalloprotein | | Authors: | Forouhar, F, Lew, S, Seetharaman, J, Mills, J.H, Khare, S.D, Everett, J.K, Baker, D, Montelione, G.T, Hunt, J.F, Tong, L, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2013-02-17 | | Release date: | 2013-03-27 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.4 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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4KY3
 | | Three-dimensional Structure of the orthorhombic crystal of computationally designed insertion domain , Northeast Structural Genomics Consortium (NESG) Target OR327 | | Descriptor: | designed protein OR327 | | Authors: | Kuzin, A, Su, M, Seetharaman, J, Maglaqui, M, Xiao, R, Lee, D, Gleixner, J, Baker, D, Everett, J.K, Acton, T.B, Montelione, G.T, Tong, L, Hunt, J.F, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2013-05-28 | | Release date: | 2013-06-19 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.964 Å) | | Cite: | Precise assembly of complex beta sheet topologies from de novo designed building blocks.
Elife, 4, 2015
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5BVB
 | | Engineered Digoxigenin binder DIG5.1a | | Descriptor: | DIG5.1a, DIGOXIGENIN | | Authors: | Doyle, L.A, Stoddard, B.L. | | Deposit date: | 2015-06-04 | | Release date: | 2015-10-28 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.
J.Chem.Inf.Model., 56, 2016
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359D
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8FLX
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7GCH
 | | STRUCTURE OF CHYMOTRYPSIN-*TRIFLUOROMETHYL KETONE INHIBITOR COMPLEXES. COMPARISON OF SLOWLY AND RAPIDLY EQUILIBRATING INHIBITORS | | Descriptor: | 1,1,1-TRIFLUORO-3-((N-ACETYL)-L-LEUCYLAMIDO)-4-PHENYL-BUTAN-2-ONE(N-ACETYL-L-LEUCYL-L-PHENYLALANYL TRIFLUOROMETHYL KETONE), GAMMA-CHYMOTRYPSIN A | | Authors: | Brady, K, Ringe, D, Abeles, R.H. | | Deposit date: | 1990-04-06 | | Release date: | 1990-10-15 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors.
Biochemistry, 29, 1990
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3FC3
 | | Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I | | Descriptor: | 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3', 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3', Restriction endonuclease Hpy99I, ... | | Authors: | Sokolowska, M, Czapinska, H, Bochtler, M. | | Deposit date: | 2008-11-21 | | Release date: | 2009-03-31 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
Nucleic Acids Res., 37, 2009
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