6DKM
 
 | | DHD131 | | Descriptor: | DHD131_A, DHD131_B | | Authors: | Bick, M.J, Chen, Z, Baker, D. | | Deposit date: | 2018-05-29 | | Release date: | 2018-12-19 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | Programmable design of orthogonal protein heterodimers.
Nature, 565, 2019
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6DM9
 | | DHD15_extended | | Descriptor: | DHD15_extended_A, DHD15_extended_B, SULFATE ION | | Authors: | Bick, M.J, Chen, Z, Baker, D. | | Deposit date: | 2018-06-04 | | Release date: | 2018-12-19 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Programmable design of orthogonal protein heterodimers.
Nature, 565, 2019
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7CBC
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4HXT
 | | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR329 | | Descriptor: | De Novo Protein OR329 | | Authors: | Vorobiev, S, Su, M, Parmeggiani, F, Seetharaman, J, Huang, P.-S, Maglaqui, M, Xiao, X, 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: | 2012-11-12 | | Release date: | 2012-11-21 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Computational design of self-assembling cyclic protein homo-oligomers.
NAT.CHEM., 9, 2017
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4QPZ
 | | Crystal structure of the formolase FLS_v2 in space group P 21 | | Descriptor: | Formolase, MAGNESIUM ION, THIAMINE DIPHOSPHATE | | Authors: | Shen, B.W, Siegel, J.B, Stoddard, B.L, Baker, D. | | Deposit date: | 2014-06-25 | | Release date: | 2015-03-11 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Computational protein design enables a novel one-carbon assimilation pathway.
Proc.Natl.Acad.Sci.USA, 112, 2015
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3U1O
 | | THREE DIMENSIONAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH19, Northeast Structural Genomics Consortium Target OR49 | | Descriptor: | De Novo design cysteine esterase ECH19, SODIUM ION, SULFATE ION | | Authors: | Kuzin, A, Su, M, Lew, S, Forouhar, F, Seetharaman, J, Daya, P, Xiao, R, Ciccosanti, C, Richter, F, Everett, J.K, Acton, T.B, Baker, D, Montelione, G.T, Hunt, J.F, Tong, L, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2011-09-30 | | Release date: | 2011-10-26 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.494 Å) | | Cite: | Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.
J.Am.Chem.Soc., 134, 2012
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3NQV
 | | Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R5 7/4A | | Descriptor: | BENZAMIDINE, deoxyribose phosphate aldolase | | 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: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
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2LPB
 | | Structure of the complex of the central activation domain of Gcn4 bound to the mediator co-activator domain 1 of Gal11/med15 | | Descriptor: | General control protein GCN4, Mediator of RNA polymerase II transcription subunit 15 | | Authors: | Brzovic, P.S, Heikaus, C.C, Kisselev, L, Vernon, R, Herbig, E, Pacheco, D, Warfield, L, Littlefield, P, Baker, D, Klevit, R.E, Hahn, S. | | Deposit date: | 2012-02-07 | | Release date: | 2012-02-22 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex.
Mol.Cell, 44, 2011
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6BF3
 | | Solution structure of de novo macrocycle design7.3a | | Descriptor: | QDP(DPR)K(2TL)(DAS) | | Authors: | Shortridge, M.D, Hosseinzadeh, P, Pardo-Avila, F, Varani, G, Baker, D. | | Deposit date: | 2017-10-25 | | Release date: | 2018-01-10 | | Last modified: | 2023-11-15 | | Method: | SOLUTION NMR | | Cite: | Comprehensive computational design of ordered peptide macrocycles.
Science, 358, 2017
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6BE7
 | | Solution structure of de novo macrocycle Design8.1 | | Descriptor: | DDPT(DPR)(DAR)Q(DGN) | | Authors: | Shortridge, M.D, Hosseinzadeh, P, Pardo-Avila, F, Varani, G, Baker, D. | | Deposit date: | 2017-10-24 | | Release date: | 2018-01-03 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Comprehensive computational design of ordered peptide macrocycles.
Science, 358, 2017
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6WHZ
 | | Histone deacetylases complex with peptide macrocycles | | Descriptor: | Histone deacetylase 2, SODIUM ION, TETRAETHYLENE GLYCOL, ... | | Authors: | Bera, A.K, Hosseinzadeh, P, Watson, P, Baker, D. | | Deposit date: | 2020-04-08 | | Release date: | 2021-04-21 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.
Nat Commun, 12, 2021
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6B87
 | | Crystal structure of transmembrane protein TMHC2_E | | Descriptor: | TMHC2_E | | Authors: | Lu, P, DiMaio, F, Min, D, Wei, K.Y, Bowie, J, Baker, D. | | Deposit date: | 2017-10-05 | | Release date: | 2018-03-14 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.947 Å) | | Cite: | Accurate computational design of multipass transmembrane proteins.
Science, 359, 2018
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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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6BF5
 | | Solution structure of de novo macrocycle design7.3a | | Descriptor: | QDP(DPR)K(DTH)(DAS) | | Authors: | Shortridge, M.D, Hosseinzadeh, P, Pardo-Avila, F, Varani, G, Baker, D. | | Deposit date: | 2017-10-25 | | Release date: | 2018-01-10 | | Last modified: | 2024-10-23 | | Method: | SOLUTION NMR | | Cite: | Comprehensive computational design of ordered peptide macrocycles.
Science, 358, 2017
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6BEO
 | | Solution structure of de novo macrocycle design9.1 | | Descriptor: | (DPR)PY(DHI)PKDL(DGN) | | Authors: | Shortridge, M.D, Hosseinzadeh, P, Pardo-Avila, F, Varani, G, Baker, D. | | Deposit date: | 2017-10-25 | | Release date: | 2017-12-27 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Comprehensive computational design of ordered peptide macrocycles.
Science, 358, 2017
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4NWN
 | | Computationally Designed Two-Component Self-Assembling Tetrahedral Cage T32-28 | | Descriptor: | Propanediol utilization: polyhedral bodies pduT, Uncharacterized protein | | Authors: | McNamara, D.E, King, N.P, Bale, J.B, Sheffler, W, Baker, D, Yeates, T.O. | | Deposit date: | 2013-12-06 | | Release date: | 2014-05-28 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (4.5 Å) | | Cite: | Accurate design of co-assembling multi-component protein nanomaterials.
Nature, 510, 2014
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5HRZ
 | | Computationally Designed Trimer 1na0C3_3 | | Descriptor: | TPR domain protein 1na0C3_3 | | Authors: | Cascio, D, McNamara, D.E, Fallas, J.A, Baker, D, Yeates, T.O. | | Deposit date: | 2016-01-24 | | Release date: | 2017-04-12 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Computational design of self-assembling cyclic protein homo-oligomers.
Nat Chem, 9, 2017
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3UZJ
 | | Designed protein KE59 R13 3/11H with benzotriazole | | Descriptor: | 1H-benzotriazole, Kemp eliminase KE59 R13 3/11H, PHOSPHATE ION | | Authors: | Khersonsky, O, Kiss, G, Roethlisberger, D, Dym, O, Albeck, S, Houk, K.N, Baker, D, Tawfik, D.S, Israel Structural Proteomics Center (ISPC) | | Deposit date: | 2011-12-07 | | Release date: | 2012-06-06 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.
Proc.Natl.Acad.Sci.USA, 109, 2012
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3UY8
 | | Designed protein KE59 R5_11/5F | | Descriptor: | Kemp eliminase KE59 R5_11/5F, SULFATE ION | | Authors: | Khersonsky, O, Kiss, G, Roethlisberger, D, Dym, O, Albeck, S, Houk, K.N, Baker, D, Tawfik, D.S, Israel Structural Proteomics Center (ISPC) | | Deposit date: | 2011-12-06 | | Release date: | 2012-06-06 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.41 Å) | | Cite: | Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.
Proc.Natl.Acad.Sci.USA, 109, 2012
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8TCG
 | | Integrin alpha-v beta-6 in complex with minibinder B6_BP_dslf | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Integrin alpha-V heavy chain, ... | | Authors: | Campbell, M.G, Fernandez, A, Roy, A, Kraft, J, Baker, D. | | Deposit date: | 2023-06-30 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | De novo design of highly selective miniprotein inhibitors of integrins alpha v beta 6 and alpha v beta 8.
Nat Commun, 14, 2023
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8GEL
 | | Cryo-EM structure of synthetic tetrameric building block sC4 | | Descriptor: | sC4 | | Authors: | Redler, R.L, Huddy, T.F, Hsia, Y, Baker, D, Ekiert, D, Bhabha, G. | | Deposit date: | 2023-03-07 | | Release date: | 2024-03-13 | | Last modified: | 2024-04-10 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Blueprinting extendable nanomaterials with standardized protein blocks.
Nature, 627, 2024
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3UXD
 | | Designed protein KE59 R1 7/10H with dichlorobenzotriazole (DBT) | | Descriptor: | 5,7-dichloro-1H-benzotriazole, Kemp eliminase KE59 R1 7/10H, PHOSPHATE ION | | Authors: | Khersonsky, O, Kiss, G, Roethlisberger, D, Dym, O, Albeck, S, Houk, K.N, Baker, D, Tawfik, D.S, Israel Structural Proteomics Center (ISPC) | | Deposit date: | 2011-12-05 | | Release date: | 2012-06-06 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.
Proc.Natl.Acad.Sci.USA, 109, 2012
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3UY7
 | | Designed protein KE59 R1 7/10H with G130S mutation | | Descriptor: | Kemp eliminase KE59 R1 7/10H, SODIUM ION, SULFATE ION | | Authors: | Khersonsky, O, Kiss, G, Roethlisberger, D, Dym, O, Albeck, S, Houk, K.N, Baker, D, Tawfik, D.S, Israel Structural Proteomics Center (ISPC) | | Deposit date: | 2011-12-06 | | Release date: | 2012-06-27 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.
Proc.Natl.Acad.Sci.USA, 109, 2012
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1MPU
 | | Crystal Structure of the free human NKG2D immunoreceptor | | Descriptor: | NKG2-D type II integral membrane protein, PHOSPHATE ION | | Authors: | McFarland, B.J, Kortemme, T, Baker, D, Strong, R.K. | | Deposit date: | 2002-09-12 | | Release date: | 2003-04-15 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Symmetry Recognizing Asymmetry: Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC
Class I-like Ligands
Structure, 11, 2003
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5TX8
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