PDB: 5605 resultsInfo pagesStatus searchChemie searchBIRD

---

6WXO	De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE Descriptor: GLYCEROL, SULFATE ION, TFD-HE Authors: Caldwell, S.J, Zeymer, C, Haydon, I.C, Huang, P, Hilvert, D, Baker, D. Deposit date: 2020-05-11 Release date: 2020-11-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.41 Å) Cite: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proc.Natl.Acad.Sci.USA, 117, 2020
5BVL	Crystal structure of a de novo designed TIM-barrel Descriptor: designed TIM barrel sTIM11 Authors: Feldmeier, K, Hocker, B. Deposit date: 2015-06-05 Release date: 2015-11-18 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (1.992 Å) Cite: De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nat.Chem.Biol., 12, 2016
6WXP	De novo TIM barrel-ferredoxin fold fusion homodimer with 4-glutamate centre TFD-EE Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, TFD-EE Authors: Caldwell, S.J, Zeymer, C, Haydon, I.C, Huang, P, Hilvert, D, Baker, D. Deposit date: 2020-05-11 Release date: 2020-11-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proc.Natl.Acad.Sci.USA, 117, 2020
6EIZ	A de novo designed hexameric coiled coil CC-Hex2 with farnesol bound in the channel. Descriptor: (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol, CC-Hex2 Authors: Rhys, G.G, Burton, A.J, Dawson, W.M, Thomas, F, Woolfson, D.N. Deposit date: 2017-09-19 Release date: 2018-07-11 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (1.85 Å) Cite: De Novo-Designed alpha-Helical Barrels as Receptors for Small Molecules. ACS Synth Biol, 7, 2018
5C2N	The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Beta propeller Authors: Smock, R.G, Yadid, I, Dym, O, Clarke, J, Tawfik, D.S. Deposit date: 2015-06-16 Release date: 2016-01-20 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (1.65 Å) Cite: De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints. Cell, 164, 2016
5C2M	The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints Descriptor: Predicted protein Authors: Smock, R.G, Yadid, I, Dym, O, Clarke, J, Tawfik, D.S. Deposit date: 2015-06-16 Release date: 2016-02-03 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (1.9 Å) Cite: De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints. Cell, 164, 2016
8BL3	De novo single-chain immunoglobulin dimer scIg12 Descriptor: GLYCEROL, scIg12 Authors: Nadal, M, Roel-Touris, J, Marcos, E. Deposit date: 2022-11-09 Release date: 2023-10-04 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops. Nat Commun, 14, 2023
7TJL	Crystal structure of de novo designed protein, SEWN0.1 Descriptor: De novo designed protein, SEWN0.1 Authors: Cummins, M.C, Jacobs, T.M, Kuhlman, B. Deposit date: 2022-01-16 Release date: 2022-06-29 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.87 Å) Cite: AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein Protein Sci., 31, 2022
6W90	De novo designed NTF2 fold protein NT-9 Descriptor: 1,2-Distearoyl-sn-glycerophosphoethanolamine, NTF2 fold protein loop-helix-loop design NT-9 Authors: Thompson, M.C, Pan, X, Liu, L, Fraser, J.S, Kortemme, T. Deposit date: 2020-03-21 Release date: 2020-08-19 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.5 Å) Cite: Expanding the space of protein geometries by computational design of de novo fold families. Science, 369, 2020
7DGW	De novo designed protein H4A2S Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, de novo designed protein H4A2S Authors: Xu, Y, Liao, S, Chen, Q, Liu, H. Deposit date: 2020-11-12 Release date: 2021-11-24 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (1.35 Å) Cite: A backbone-centred energy function of neural networks for protein design. Nature, 602, 2022
1LQ7	De Novo Designed Protein Model of Radical Enzymes Descriptor: Alpha3W Authors: Dai, Q.-H, Tommos, C, Fuentes, E.J, Blomberg, M, Dutton, P.L, Wand, A.J. Deposit date: 2002-05-09 Release date: 2002-06-05 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Structure of a De Novo Designed Protein Model of Radical Enzymes J.Am.Chem.Soc., 124, 2002
5E6G	Crystal Structure of De Novo Designed Protein CA01 Descriptor: De novo designed protein CA01, GLYCEROL, PHOSPHATE ION Authors: Jacobs, T.M, Williams, T, Kuhlman, B. Deposit date: 2015-10-09 Release date: 2016-05-18 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (2.09 Å) Cite: Design of structurally distinct proteins using strategies inspired by evolution. Science, 352, 2016
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: 2016-02-17 Method: X-RAY DIFFRACTION (2.964 Å) Cite: Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife, 4, 2015
2LRH	Solution NMR structure of de novo designed protein, p-loop ntpase fold, Northeast Structural Genomics Consortium target or137 Descriptor: De novo designed protein Authors: Liu, G, Koga, N, Koga, R, Xiao, R, Lee, H, Janjua, H, Kohan, E, Acton, T.B, Everett, J.K, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) Deposit date: 2012-03-30 Release date: 2012-07-04 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Solution NMR structure of de novo designed protein, p-loop ntpase fold, Northeast Structural Genomics Consortium target or137 To be Published
2N75	Solution NMR Structure of De novo designed protein, Rossmann2x2 Fold, Northeast Structural Genomics Consortium (NESG) Target OR446 Descriptor: De novo designed protein Authors: Liu, G, Lin, Y, Koga, N, Koga, R, Xiao, R, Janjua, H, Pederson, K, Acton, T.B, Kornhaber, G, Everett, J.K, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) Deposit date: 2015-09-03 Release date: 2016-01-27 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Solution NMR Structure of De novo designed protein, Rossmann2x2 Fold, Northeast Structural Genomics Consortium (NESG) Target OR446 To be Published
8BL6	De novo single-chain immunoglobulin dimer scIg12+EF3a Descriptor: GLYCEROL, TERBIUM(III) ION, dIG14-scdim-EF62 Authors: Nadal, M, Roel-Touris, J, Marcos, E. Deposit date: 2022-11-09 Release date: 2023-10-04 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops. Nat Commun, 14, 2023
2MTL	Solution NMR Structure of De novo designed FR55, Northeast Structural Genomics Consortium (NESG) Target OR109 Descriptor: De novo designed protein FR55 OR109 Authors: Liu, G, Koga, N, Koga, R, Xiao, R, Hamilton, K, Ciccosanti, C, Sahdev, S, Kohan, E, Acton, T.B, Kornhaber, G, Everett, J.K, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) Deposit date: 2014-08-19 Release date: 2014-10-29 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Solution NMR Structure of De novo designed FR55, Northeast Structural Genomics Consortium (NESG) Target OR109 To be Published
6XEH	Solution NMR Structure of DE NOVO DESIGNED Rossmann 2x3 Fold Protein r2x3_168, Northeast Structural Genomics Consortium (NESG) Target OR386 Descriptor: DE NOVO DESIGNED OR386 Authors: Liu, G, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) Deposit date: 2020-06-12 Release date: 2020-08-05 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Role of backbone strain in de novo design of complex alpha/beta protein structures Accurate de novo design of asymetric alpha/beta proteins with ten or more secondary structure elements requires consideration of backbone strain Design principle proposed from designed larger alpha/beta-proteins not folded as designed: Consistency between local, non-local, and global structures To Be Published
6X8N	Crystal Structure of H49A ABLE mutant Descriptor: De novo designed ABLE protein Authors: Polizzi, N.F. Deposit date: 2020-06-01 Release date: 2020-08-26 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.6 Å) Cite: A defined structural unit enables de novo design of small-molecule-binding proteins. Science, 369, 2020
6ZV9	Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and tryptophan antenna (TFD-EE N6W) Descriptor: 1,2-ETHANEDIOL, TERBIUM(III) ION, TFD-EE Authors: Caldwell, S, Haydon, I, Piperidou, N, Huang, P, Hilvert, D, Baker, D, Zeymer, C. Deposit date: 2020-07-24 Release date: 2020-11-25 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (1.85 Å) Cite: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proc.Natl.Acad.Sci.USA, 117, 2020
7KBQ	Solution NMR Structure of DE NOVO DESIGNED Rossmann 3x3 Fold Protein r3x3_bp3, Northeast Structural Genomics Consortium (NESG) Target OR689 Descriptor: DE NOVO DESIGNED OR689 Authors: Liu, G, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) Deposit date: 2020-10-02 Release date: 2021-05-19 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Role of backbone strain in de novo design of complex alpha/beta protein structures Accurate de novo design of asymetric alpha/beta proteins with ten or more secondary structure elements requires consideration of backbone strain Design principle proposed from designed larger alpha/beta-proteins not folded as designed: Consistency between local, non-local, and global structures To Be Published
6ZT1	Two states of a de novo hexameric coiled coil assembly CC-Type2-(LaIdGe)4 Descriptor: CC-Type2-(LaIdGe)4 Authors: Rhys, G.G, Brady, R.L, Woolfson, D.N. Deposit date: 2020-07-17 Release date: 2021-02-03 Last modified: 2021-04-07 Method: X-RAY DIFFRACTION (2.01 Å) Cite: Structural resolution of switchable states of a de novo peptide assembly. Nat Commun, 12, 2021
7A8S	de novo designed ba8-barrel sTIM11 with an alpha-helical extension Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, sTIM11_h3 Authors: Shanmugaratnam, S, Wiese, J.G, Hocker, B. Deposit date: 2020-08-31 Release date: 2021-03-24 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.58 Å) Cite: Extension of a de novo TIM barrel with a rationally designed secondary structure element. Protein Sci., 30, 2021
8R8N	Hallucinated de novo TIM barrel with two helical extensions - HalluTIM2-2 Descriptor: HalluTIM2-2, SULFATE ION Authors: Beck, J, Shanmugaratnam, S, Hocker, B. Deposit date: 2023-11-29 Release date: 2024-05-22 Method: X-RAY DIFFRACTION (2.55 Å) Cite: Diversifying de novo TIM barrels by hallucination. Protein Sci., 33, 2024
8R8O	Hallucinated de novo TIM barrel with three helical extensions - HalluTIM3-1 Descriptor: ACETATE ION, CHLORIDE ION, GLYCEROL, ... Authors: Beck, J, Shanmugaratnam, S, Hocker, B. Deposit date: 2023-11-29 Release date: 2024-05-22 Method: X-RAY DIFFRACTION (2.15 Å) Cite: Diversifying de novo TIM barrels by hallucination. Protein Sci., 33, 2024

<12345678910111213141516>