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3UD6
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BU of 3ud6 by Molmil
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
8F6R
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BU of 8f6r by Molmil
CryoEM structure of designed modular protein oligomer C6-79
Descriptor: De novo designed oligomeric protein C6-79
Authors:Redler, R.L, Edman, N.I, Baker, D, Ekiert, D, Bhabha, G.
Deposit date:2022-11-17
Release date:2023-11-29
Last modified:2024-07-24
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Cell, 187, 2024
8F6Q
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BU of 8f6q by Molmil
CryoEM structure of designed modular protein oligomer C8-71
Descriptor: C8-71
Authors:Redler, R.L, Edman, N.I, Baker, D, Ekiert, D, Bhabha, G.
Deposit date:2022-11-17
Release date:2023-11-29
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Cell, 187, 2024
9MRB
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BU of 9mrb by Molmil
The designed serine hydrolase known as dad_t1
Descriptor: TETRAETHYLENE GLYCOL, dad_t1
Authors:Pellock, S.J, Lauko, A, Bera, A, Baker, D.
Deposit date:2025-01-07
Release date:2025-02-19
Last modified:2025-04-30
Method:X-RAY DIFFRACTION (2 Å)
Cite:Computational design of serine hydrolases.
Science, 388, 2025
4LNY
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BU of 4lny by Molmil
Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR422
Descriptor: CADMIUM ION, CHLORIDE ION, Engineered Protein OR422
Authors:Vorobiev, S, Su, M, Bjelic, S, Kipnis, Y, Wang, L, Sahdev, S, Xiao, R, Maglaqui, M, Kogan, S, Baker, D, Everett, J.K, Acton, T.B, Montelione, G.T, Hunt, J.F, Tong, L, Northeast Structural Genomics Consortium (NESG)
Deposit date:2013-07-12
Release date:2013-08-07
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (1.929 Å)
Cite:Crystal Structure of Engineered Protein OR422.
To be Published
7FB8
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BU of 7fb8 by Molmil
De Novo-Designed and Disulfide-Bridged Peptide Heterodimer - hd1
Descriptor: ASP-ASP-LYS-ASP-CYS-ASP-GLU-TYR-CYS-LYS-LYS-THR-LYS-GLU-NH2, GLU-LE1-THR-GLY-HIS-ILE-GLU-GLY-PRO-THR-LE1-THR-LE1-HIS-CYS-LYS-NH2
Authors:Yao, H, Yao, S, Zheng, Y, Moyer, A, Baker, D, Wu, C.
Deposit date:2021-07-08
Release date:2022-05-18
Last modified:2023-11-15
Method:SOLUTION NMR
Cite:De novo design and directed folding of disulfide-bridged peptide heterodimers.
Nat Commun, 13, 2022
7FBA
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BU of 7fba by Molmil
De Novo-Designed and Disulfide-Bridged Peptide Heterodimer - hd2
Descriptor: ALA-LE1-CYS-GLU-CYS-GLY-PRO-THR-ARG-GLU-CYS-LYS-NH2, GLU-CYS-ARG-GLU-TYR-GLY-PRO-LE1-LYS-LE1-LE1-ALA-NH2
Authors:Yao, H, Yao, S, Moyer, A, Zheng, Y, Baker, D, Wu, C.
Deposit date:2021-07-08
Release date:2022-05-18
Last modified:2023-11-15
Method:SOLUTION NMR
Cite:De novo design and directed folding of disulfide-bridged peptide heterodimers.
Nat Commun, 13, 2022
3J1W
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BU of 3j1w by Molmil
A refined model of the prototypical Salmonella typhimurium T3SS basal body reveals the molecular basis for its assembly
Descriptor: Protein PrgH
Authors:Sgourakis, N.G, Worrall, L.J, Strynadka, N.C.J, Baker, D.
Deposit date:2012-07-10
Release date:2013-05-22
Last modified:2024-02-21
Method:ELECTRON MICROSCOPY (11.7 Å)
Cite:A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.
Plos Pathog., 9, 2013
3J3X
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BU of 3j3x by Molmil
Independent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (training map)
Descriptor: Chaperonin
Authors:DiMaio, F, Zhang, J, Chiu, W, Baker, D.
Deposit date:2013-05-02
Release date:2013-05-29
Last modified:2024-02-21
Method:ELECTRON MICROSCOPY (4.3 Å)
Cite:Cryo-EM model validation using independent map reconstructions.
Protein Sci., 22, 2013
4UOT
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BU of 4uot by Molmil
Thermodynamic hyperstability in parametrically designed helical bundles
Descriptor: DESIGNED HELICAL BUNDLE 5H2L
Authors:Oberdorfer, G, Huang, P, Pei, X.Y, Xu, C, Gonen, T, Nannenga, B, DiMaio, D, Rogers, J, Luisi, B.F, Baker, D.
Deposit date:2014-06-09
Release date:2014-11-05
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:High Thermodynamic Stability of Parametrically Designed Helical Bundles
Science, 346, 2014
4D49
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BU of 4d49 by Molmil
Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.
Descriptor: ARGININE, ARMADILLO REPEAT PROTEIN ARM00027, POLY ARG DECAPEPTIDE
Authors:Reichen, C, Forzani, C, Zhou, T, Parmeggiani, F, Fleishman, S.J, Mittl, P.R.E, Madhurantakam, C, Honegger, A, Ewald, C, Zerbe, O, Baker, D, Caflisch, A, Pluckthun, A.
Deposit date:2014-10-27
Release date:2016-01-13
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.
J.Mol.Biol., 428, 2016
4D4E
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BU of 4d4e by Molmil
Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.
Descriptor: ARMADILLO REPEAT PROTEIN ARM00016, GLYCEROL
Authors:Reichen, C, Forzani, C, Zhou, T, Parmeggiani, F, Fleishman, S.J, Mittl, P.R.E, Madhurantakam, C, Honegger, A, Ewald, C, Zerbe, O, Baker, D, Caflisch, A, Pluckthun, A.
Deposit date:2014-10-28
Release date:2016-01-13
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.
J.Mol.Biol., 428, 2016
4UOS
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BU of 4uos by Molmil
Thermodynamic hyperstability in parametrically designed helical bundles
Descriptor: DESIGNED HELICAL BUNDLE
Authors:Oberdorfer, G, Huang, P, Pei, X.Y, Xu, C, Gonen, T, Nannenga, B, DiMaio, D, Rogers, J, Luisi, B.F, Baker, D.
Deposit date:2014-06-09
Release date:2014-11-05
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:High Thermodynamic Stability of Parametrically Designed Helical Bundles
Science, 346, 2014
4DDF
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BU of 4ddf by Molmil
Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group P4
Descriptor: CHLORIDE ION, Propanediol utilization polyhedral body protein PduT, SULFATE ION
Authors:Sawaya, M.R, King, N.P, Sheffler, W, Baker, D, Yeates, T.O.
Deposit date:2012-01-18
Release date:2012-06-06
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (3.15 Å)
Cite:Computational design of self-assembling protein nanomaterials with atomic level accuracy.
Science, 336, 2012
6TMS
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BU of 6tms by Molmil
Crystal structure of a de novo designed hexameric helical-bundle protein
Descriptor: SULFATE ION, a novel designed pore protein, affinity purification tag
Authors:Xu, C, Pei, X.Y, Luisi, B.F, Baker, D.
Deposit date:2019-12-05
Release date:2020-04-29
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Computational design of transmembrane pores.
Nature, 585, 2020
6TJ1
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BU of 6tj1 by Molmil
Crystal structure of a de novo designed hexameric helical-bundle protein
Descriptor: De novo designed WSHC6, purification tag
Authors:Xu, C, Pei, X.Y, Luisi, B.F, Baker, D.
Deposit date:2019-11-23
Release date:2020-04-29
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Computational design of transmembrane pores.
Nature, 585, 2020
2VLO
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BU of 2vlo by Molmil
K97A mutant of E9 DNase domain in complex with Im9
Descriptor: COLICIN E9, COLICIN-E9 IMMUNITY PROTEIN, SULFATE ION
Authors:Keeble, A.H, Joachimiak, L.A, Mate, M.J, Meenan, N, Kirkpatrick, N, Baker, D, Kleanthous, C.
Deposit date:2008-01-15
Release date:2008-05-20
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases.
J.Mol.Biol., 379, 2008
5KBA
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BU of 5kba by Molmil
Computational Design of Self-Assembling Cyclic Protein Homooligomers
Descriptor: Designed protein ANK1C2
Authors:Sankaran, B, Zwart, P.H, Fallas, J.A, Pereira, J.H, Ueda, G, Baker, D.
Deposit date:2016-06-02
Release date:2017-04-12
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.601 Å)
Cite:Computational design of self-assembling cyclic protein homo-oligomers.
Nat Chem, 9, 2017
5KCI
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BU of 5kci by Molmil
Crystal Structure of HTC1
Descriptor: GLYCEROL, SULFATE ION, Uncharacterized protein YPL067C, ...
Authors:Martin, R.M, Horowitz, S, Koepnick, B, Cooper, S, Flatten, J, Rogawski, D.S, Koropatkin, N.M, Beinlich, F.R.M, Players, F, Students, U.M, Popovic, Z, Baker, D, Khatib, F, Bardwell, J.C.A.
Deposit date:2016-06-06
Release date:2016-09-21
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (1.833 Å)
Cite:Determining crystal structures through crowdsourcing and coursework.
Nat Commun, 7, 2016
5K7V
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BU of 5k7v by Molmil
Computational Design of Self-Assembling Cyclic Protein Homooligomers
Descriptor: Designed protein HR00C3
Authors:Sankaran, B, Zwart, P.H, Fallas, J.A, Pereira, J.H, Ueda, G, Baker, D.
Deposit date:2016-05-26
Release date:2017-04-12
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (3.165 Å)
Cite:Computational design of self-assembling cyclic protein homo-oligomers.
Nat Chem, 9, 2017
2VLQ
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BU of 2vlq by Molmil
F86A mutant of E9 DNase domain in complex with Im9
Descriptor: COLICIN E9, COLICIN-E9 IMMUNITY PROTEIN, MALONIC ACID
Authors:Keeble, A.H, Joachimiak, L.A, Mate, M.J, Meenan, N, Kirkpatrick, N, Baker, D, Kleanthous, C.
Deposit date:2008-01-15
Release date:2008-05-20
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases.
J.Mol.Biol., 379, 2008
6E9X
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BU of 6e9x by Molmil
DHF91 filament
Descriptor: DHF91 filament
Authors:Lynch, E.M, Shen, H, Fallas, J.A, Kollman, J.M, Baker, D.
Deposit date:2018-08-01
Release date:2018-11-21
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (7.8 Å)
Cite:De novo design of self-assembling helical protein filaments.
Science, 362, 2018
5JI4
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BU of 5ji4 by Molmil
Solution structure of the de novo mini protein gEEHE_02
Descriptor: W37
Authors:Buchko, G.W, Bahl, C.D, Pulavarti, S.V, Baker, D, Szyperski, T.
Deposit date:2016-04-21
Release date:2016-09-28
Last modified:2024-10-23
Method:SOLUTION NMR
Cite:Accurate de novo design of hyperstable constrained peptides.
Nature, 538, 2016
5JHI
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BU of 5jhi by Molmil
Solution structure of the de novo mini protein gEHE_06
Descriptor: W35
Authors:Buchko, G.W, Bahl, C.D, Gilmore, J.M, Pulavarti, S.V, Baker, D, Szyperski, T.
Deposit date:2016-04-21
Release date:2016-09-28
Last modified:2024-10-23
Method:SOLUTION NMR
Cite:Accurate de novo design of hyperstable constrained peptides.
Nature, 538, 2016
5WP3
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BU of 5wp3 by Molmil
Crystal Structure of EED in complex with EB22
Descriptor: EB22, Polycomb protein EED, UNKNOWN ATOM OR ION
Authors:Dong, C, Tempel, W, Zhu, L, Moody, J.D, Baker, D, Bountra, C, Arrowsmith, C.H, Edwards, A.M, Min, J, Structural Genomics Consortium (SGC)
Deposit date:2017-08-03
Release date:2017-09-13
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017

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PDB entries from 2025-07-09

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