Author results

5TVY
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COMPUTATIONALLY DESIGNED FENTANYL BINDER - FEN49
Descriptor:Endo-1,4-beta-xylanase A, 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
Authors:Bick, M.J., Greisen, P.J., Morey, K.J., Antunes, M.S., La, D., Sankaran, B., Reymond, L., Johnsson, K., Medford, J.I., Baker, D.
Deposit date:2016-11-10
Release date:2017-10-04
Method:X-RAY DIFFRACTION (1 Å)
Cite:Computational design of environmental sensors for the potent opioid fentanyl.
Elife, 6, 2017
4A29
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STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.0
Descriptor:ENGINEERED RETRO-ALDOL ENZYME RA95.0, 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE, D-MALATE
Authors:Giger, L., Caner, S., Kast, P., Baker, D., Ban, N., Hilvert, D.
Deposit date:2011-09-23
Release date:2012-11-07
Last modified:2019-05-15
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Evolution of a designed retro-aldolase leads to complete active site remodeling.
Nat.Chem.Biol., 9, 2013
5AN7
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STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5-8F WITH A BOUND 1,3-DIKETONE INHIBITOR
Descriptor:RA95.5-8F, PHOSPHATE ION, (2E)-1-(6-methoxynaphthalen-2-yl)but-2-en-1-one
Authors:Obexer, R., Mittl, P.R.E., Hilvert, D.
Deposit date:2015-09-04
Release date:2016-08-17
Last modified:2019-05-22
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase.
Nat Chem, 9, 2017
5AOU
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STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5-8F APO
Descriptor:INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE, 1,2-ETHANEDIOL, PHOSPHATE ION
Authors:Obexer, R., Mittl, P., Hilvert, D.
Deposit date:2015-09-11
Release date:2016-08-17
Last modified:2019-05-08
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase.
Nat Chem, 9, 2017
6MRR
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DE NOVO DESIGNED PROTEIN FOLDIT1
Descriptor:Foldit1
Authors:Koepnick, B., Bick, M.J., Estep, R.D., Kleinfelter, S., Wei, L., Baker, D.
Deposit date:2018-10-15
Release date:2019-06-12
Last modified:2019-06-26
Method:X-RAY DIFFRACTION (1.18 Å)
Cite:De novo protein design by citizen scientists.
Nature, 570, 2019
5CWG
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CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR10
Descriptor:Designed helical repeat protein, 1,2-ETHANEDIOL, UNKNOWN LIGAND
Authors:Bhabha, G., Ekiert, D.C.
Deposit date:2015-07-28
Release date:2015-12-16
Last modified:2016-01-06
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Exploring the repeat protein universe through computational protein design.
Nature, 528, 2015
5V2O
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DE NOVO DESIGN OF NOVEL COVALENT CONSTRAINED MESO-SIZE PEPTIDE SCAFFOLDS WITH UNIQUE TERTIARY STRUCTURES
Descriptor:TP2, SULFATE ION, NONAETHYLENE GLYCOL, ...
Authors:Dang, B., Wu, H., Mulligan, V.K., Mravic, M., Wu, Y., Lemmin, T., Ford, A., Silva, D., Baker, D., DeGrado, W.F.
Deposit date:2017-03-06
Release date:2017-10-04
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
6MOG
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DIMERIC DARPIN C_R3
Descriptor:DARPin C_R3, 1,2-ETHANEDIOL, TRIETHYLENE GLYCOL
Authors:Jude, K.M., Mohan, K., Garcia, K.C.
Deposit date:2018-10-04
Release date:2019-06-05
Last modified:2019-06-12
Method:X-RAY DIFFRACTION (1.21 Å)
Cite:Topological control of cytokine receptor signaling induces differential effects in hematopoiesis.
Science, 364, 2019
4OU1
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CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED RETRO-ALDOLASE COVALENTLY BOUND TO FOLDING PROBE 1 [(6-METHOXYNAPHTHALEN-2-YL)(OXIRAN-2-YL)METHANOL]
Descriptor:Retro-aldolase, design RA114, (1S,2S)-1-(6-methoxynaphthalen-2-yl)propane-1,2-diol, ...
Authors:Bhabha, G., Zhang, X., Ekiert, D.C.
Deposit date:2014-02-14
Release date:2014-03-05
Last modified:2014-04-23
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts.
Proc.Natl.Acad.Sci.USA, 111, 2014
5A0E
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CRYSTAL STRUCTURE OF CYCLOPHILIN D IN COMPLEX WITH CSA ANALOGUE, JW47.
Descriptor:PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL, JW47
Authors:Warne, J., Pryce, G., Hill, J., Shi, X., Lenneras, F., Puentes, F., Kip, M., Hilditch, L., Walker, P., Simone, M., Chan, A.W.E., Towers, G., Coker, A.R., Duchen, M., Szabadkai, G., Baker, D., Selwood, D.L.
Deposit date:2015-04-19
Release date:2015-12-30
Last modified:2019-05-08
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Selective Inhibition of the Mitochondrial Permeability Transition Pore Protects Against Neuro-Degeneration in Experimental Multiple Sclerosis.
J.Biol.Chem., 291, 2016
5CWC
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CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR5
Descriptor:Designed helical repeat protein, 1,2-ETHANEDIOL
Authors:Bhabha, G., Ekiert, D.C.
Deposit date:2015-07-27
Release date:2015-12-16
Last modified:2016-01-06
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Exploring the repeat protein universe through computational protein design.
Nature, 528, 2015
4J4Z
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CRYSTAL STRUCTURE OF THE IMPROVED VARIANT OF THE EVOLVED SERINE HYDROLASE, OSH55.4_H1.2, BOND WITH SULFATE ION IN THE ACTIVE SITE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR301
Descriptor:Designed serine hydrolase variant OSH55.4_H1.2, SULFATE ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Kuzin, A.P., Lew, S., Rajagopalan, S., Maglaqui, M., Xiao, R., Lee, D., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
Deposit date:2013-02-07
Release date:2013-03-06
Method:X-RAY DIFFRACTION (1.26 Å)
Cite:Crystal structure of the improved variant of the evolved serine hydrolase, OSH55.4_H1.2, bond with sulfate ion in the active site, Northeast Structural Genomics Consortium (NESG) Target OR301
To be Published
6MSQ
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CRYSTAL STRUCTURE OF PRO-2.3
Descriptor:pRO-2.3
Authors:Boyken, S.E., Bick, M.J., Baker, D.
Deposit date:2018-10-17
Release date:2019-05-08
Last modified:2019-05-29
Method:X-RAY DIFFRACTION (1.28 Å)
Cite:De novo design of tunable, pH-driven conformational changes.
Science, 364, 2019
6NE2
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DESIGNED REPEAT PROTEIN IN COMPLEX WITH FZ7
Descriptor:Designed repeat protein binder, Frizzled-7, ACETATE ION, ...
Authors:Miao, Y., Jude, K.M., Garcia, K.C.
Deposit date:2018-12-15
Release date:2019-05-15
Last modified:2019-06-19
Method:X-RAY DIFFRACTION (1.299 Å)
Cite:Receptor subtype discrimination using extensive shape complementary designed interfaces.
Nat.Struct.Mol.Biol., 26, 2019
4FB7
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THE APO FORM OF IDOLE-3-GLYCEROL PHOSPHATE SYNTHASE (TRPC) FORM MYCOBACTERIUM TUBERCULOSIS
Descriptor:Indole-3-glycerol phosphate synthase, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Authors:Michalska, K., Chhor, G., Jedrzejczak, R., Terwilliger, T.C., Rubin, E.J., Guinn, K., Baker, D., Ioerger, T.R., Sacchettini, J.C., Joachimiak, A., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI), Midwest Center for Structural Genomics (MCSG)
Deposit date:2012-05-22
Release date:2012-06-13
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:The apo form of idole-3-glycerol phosphate synthase (TrpC) form Mycobacterium tuberculosis
To be Published
5CWH
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CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR14
Descriptor:Designed helical repeat protein, 1,2-ETHANEDIOL
Authors:Bhabha, G., Ekiert, D.C.
Deposit date:2015-07-28
Release date:2015-12-16
Last modified:2016-01-06
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Exploring the repeat protein universe through computational protein design.
Nature, 528, 2015
4A2R
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STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5-5
Descriptor:INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE, 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE
Authors:Giger, L., Caner, S., Kast, P., Baker, D., Ban, N., Hilvert, D.
Deposit date:2011-09-28
Release date:2012-11-07
Last modified:2019-05-15
Method:X-RAY DIFFRACTION (1.302 Å)
Cite:Evolution of a designed retro-aldolase leads to complete active site remodeling.
Nat.Chem.Biol., 9, 2013
3RPT
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CRYSTAL STRUCTURE OF THE ANTI-HIV B12 SCAFFOLD PROTEIN
Descriptor:Endoglucanase E-2, SULFATE ION
Authors:Chen, L., Kwong, P.D.
Deposit date:2011-04-27
Release date:2011-12-21
Last modified:2017-07-26
Method:X-RAY DIFFRACTION (1.303 Å)
Cite:Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Science, 334, 2011
3JVE
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CRYSTAL STRUCTURE OF THE SIXTH BRCT DOMAIN OF TOPBP1
Descriptor:DNA topoisomerase 2-binding protein 1
Authors:Leung, C.C., Kellogg, E., Baker, D., Glover, J.N.M.
Deposit date:2009-09-16
Release date:2010-01-19
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (1.34 Å)
Cite:Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIbeta binding protein 1.
Protein Sci., 19, 2010
4JLL
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CRYSTAL STRUCTURE OF THE EVOLVED VARIANT OF THE COMPUTATIONALLY DESIGNED SERINE HYDROLASE, OSH55.4_H1 COVALENTLY BOUND WITH FP-ALKYNE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR273
Descriptor:Evolved variant of computationally designed serine hydrolase OSH55.4_H1, ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate, CHLORIDE ION, ...
Authors:Kuzin, A., Lew, S., Rajagopalan, S., Seetharaman, J., Tong, S., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
Deposit date:2013-03-12
Release date:2013-04-10
Last modified:2014-05-14
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:Design of activated serine-containing catalytic triads with atomic-level accuracy.
Nat.Chem.Biol., 10, 2014
3NQ8
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION R4 8/5A
Descriptor:deoxyribose phosphate aldolase, NITRATE ION, BENZAMIDINE
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Last modified:2014-03-19
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
4A2S
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STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5
Descriptor:INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE, 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE
Authors:Giger, L., Caner, S., Kast, P., Baker, D., Ban, N., Hilvert, D.
Deposit date:2011-09-28
Release date:2012-11-07
Last modified:2019-05-15
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Evolution of a designed retro-aldolase leads to complete active site remodeling.
Nat.Chem.Biol., 9, 2013
4J9T
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CRYSTAL STRUCTURE OF A PUTATIVE, DE NOVO DESIGNED UNNATURAL AMINO ACID DEPENDENT METALLOPROTEIN, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR61
Descriptor:designed unnatural amino acid dependent metalloprotein, GLYCEROL, ARSENIC
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:2019-07-17
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
5BRW
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CATALYTIC IMPROVEMENT OF AN ARTIFICIAL METALLOENZYME BY COMPUTATIONAL DESIGN
Descriptor:Carbonic anhydrase 2, ZINC ION, SULFATE ION, ...
Authors:Heinisch, T., Pellizzoni, M., Duerrenberger, M., Tinberg, C.E., Koehler, V., Klehr, J., Haeussinger, D., Baker, D., Ward, T.R.
Deposit date:2015-06-01
Release date:2015-06-17
Last modified:2015-08-26
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design.
J.Am.Chem.Soc., 137, 2015
6DG4
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STRUCTURE OF THE CHAETOMIUM THERMOPHILUM ULP1-LIKE SUMO PROTEASE CATALYTIC DOMAIN
Descriptor:Ulp1-like SUMO protease, SULFATE ION, GLYCEROL
Authors:Lima, C.D., Baytshtok, V.
Deposit date:2018-05-16
Release date:2018-07-11
Last modified:2018-09-05
Method:X-RAY DIFFRACTION (1.442 Å)
Cite:Discovery and engineering of enhanced SUMO protease enzymes.
J. Biol. Chem., 293, 2018