PDB: 5515 resultsInfo pagesStatus searchChemie searchBIRD

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7Q1S	A de novo designed hetero-dimeric antiparallel coiled coil apCC-Di-AB_var Descriptor: 1,2-ETHANEDIOL, apCC-Di-A_var, apCC-Di-B_var Authors: Shanmugaratnam, S, Rhys, G.G, Dawson, W.M, Woolfson, D.N, Hocker, B. Deposit date: 2021-10-20 Release date: 2022-07-20 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (1.99 Å) Cite: De novo designed peptides for cellular delivery and subcellular localisation. Nat.Chem.Biol., 18, 2022
7Q1T	A de novo designed hetero-dimeric antiparallel coiled coil apCC-Di-AB Descriptor: N-PROPANOL, SULFATE ION, apCC-Di-A, ... Authors: Shanmugaratnam, S, Rhys, G.G, Dawson, W.M, Woolfson, D.N, Hocker, B. Deposit date: 2021-10-20 Release date: 2022-07-20 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (1.68 Å) Cite: De novo designed peptides for cellular delivery and subcellular localisation. Nat.Chem.Biol., 18, 2022
7UEK	Crystal structure of a de novo designed ovoid TIM barrel OT3 Descriptor: OT3 Authors: Chu, A.E, Fernandez, D, Huang, P.-S. Deposit date: 2022-03-21 Release date: 2023-01-18 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.1 Å) Cite: De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design. Biodes Res, 2022, 2022
7UR7	17_bp_sh3, a small beta-barrel de novo designed protein Descriptor: 17_bp_sh3 Authors: Bera, A.K, Kim, D, Baker, D. Deposit date: 2022-04-21 Release date: 2023-03-22 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.21 Å) Cite: De novo design of small beta barrel proteins. Proc.Natl.Acad.Sci.USA, 120, 2023
7UR8	170_h_ob, a small beta-barrel de novo designed protein Descriptor: 170_h_ob Authors: Bera, A.K, Kim, D, Baker, D. Deposit date: 2022-04-21 Release date: 2023-03-22 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.5 Å) Cite: De novo design of small beta barrel proteins. Proc.Natl.Acad.Sci.USA, 120, 2023
6VG7	De novo designed Rossmann fold protein ROS2_49223 Descriptor: De novo designed protein RO2_25 Authors: Pan, X, Zhang, Y, Kelly, M, Kortemme, T. Deposit date: 2020-01-07 Release date: 2020-08-19 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Expanding the space of protein geometries by computational design of de novo fold families. Science, 369, 2020
6VGA	De novo designed Rossmann fold protein ROS2_835 Descriptor: De novo designed protein RO2_1 Authors: Pan, X, Zhang, Y, Kelly, M, Kortemme, T. Deposit date: 2020-01-07 Release date: 2020-08-19 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Expanding the space of protein geometries by computational design of de novo fold families. Science, 369, 2020
6VGB	De novo designed Rossmann fold protein ROS2_36830 Descriptor: De novo designed protein RO2_20 Authors: Pan, X, Zhang, Y, Kelly, M, Kortemme, T. Deposit date: 2020-01-07 Release date: 2020-08-19 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Expanding the space of protein geometries by computational design of de novo fold families. Science, 369, 2020
6DG5	Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb and IL-2Rg Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cytokine receptor common subunit gamma, ... Authors: Jude, K.M, Silva, D.-A, Yu, S, Baker, D, Garcia, K.C. Deposit date: 2018-05-16 Release date: 2019-01-16 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.516 Å) Cite: De novo design of potent and selective mimics of IL-2 and IL-15. Nature, 565, 2019
6DG6	Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic Descriptor: Neoleukin-2/15 Authors: Jude, K.M, Silva, D.-A, Yu, S, Baker, D, Garcia, K.C. Deposit date: 2018-05-16 Release date: 2019-01-16 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.999 Å) Cite: De novo design of potent and selective mimics of IL-2 and IL-15. Nature, 565, 2019
8SK7	Cryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43) Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, HA_20 minibinder (RFdiffusion-designed), ... Authors: Borst, A.J, Bennett, N.R. Deposit date: 2023-04-18 Release date: 2023-06-14 Last modified: 2023-09-13 Method: ELECTRON MICROSCOPY (2.93 Å) Cite: De novo design of protein structure and function with RFdiffusion. Nature, 620, 2023
6UU8	E. coli mutant sigma-S transcription initiation complex with a 7-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, and CTP for 30 minutes) Descriptor: DIPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.4 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
8UBG	DpHF19 filament Descriptor: DpHF19,Green fluorescent protein (Fragment) Authors: Lynch, E.M, Shen, H, Kollman, J.M, Baker, D. Deposit date: 2023-09-22 Release date: 2024-04-10 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: De novo design of pH-responsive self-assembling helical protein filaments. Nat Nanotechnol, 2024
6UTW	E. coli sigma-S transcription initiation complex with a 4-nt RNA ("Fresh" crystal) Descriptor: DIPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.854 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU0	E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching GTP ("Fresh" crystal soaked with GTP for 1 hour) Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.9 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
8UAO	DpHF18 filament Descriptor: DpHF18 Authors: Lynch, E.M, Shen, H, Kollman, J.M, Baker, D. Deposit date: 2023-09-21 Release date: 2024-04-10 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: De novo design of pH-responsive self-assembling helical protein filaments. Nat Nanotechnol, 2024
8UB3	DpHF7 filament Descriptor: DpHF7 filament Authors: Lynch, E.M, Farrell, D, Shen, H, Kollman, J.M, DiMaio, F, Baker, D. Deposit date: 2023-09-22 Release date: 2024-04-10 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: De novo design of pH-responsive self-assembling helical protein filaments. Nat Nanotechnol, 2024
7R1E	Mosquitocidal Cry11Ba determined at pH 10.4 from naturally-occurring nanocrystals by Serial femtosecond crystallography Descriptor: GLYCEROL, Pesticidal crystal protein Cry11Ba Authors: Colletier, J.-P, Sawaya, M.R, Schibrowsky, N.A, Cascio, D, Rodriguez, J.A. Deposit date: 2022-02-02 Release date: 2022-07-27 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.65 Å) Cite: De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals. Nat Commun, 13, 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
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
7JH6	De novo designed two-domain di-Zn(II) and porphyrin-binding protein Descriptor: NONAETHYLENE GLYCOL, Two-domain di-Zn(II) and porphyrin-binding protein, ZINC ION, ... Authors: Schmidt, N, Liu, L, DeGrado, W.F. Deposit date: 2020-07-20 Release date: 2020-12-09 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (3.5 Å) Cite: Allosteric cooperation in a de novo-designed two-domain protein. Proc.Natl.Acad.Sci.USA, 117, 2020
8AH9	De novo retro-aldolase RAbetaB-16.1 Descriptor: BENZOIC ACID, RAbetaB-16.1 Authors: Mittl, P, Oualb Chaib, A, Hilvert, D. Deposit date: 2022-07-21 Release date: 2023-08-16 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.747 Å) Cite: Design and optimization of enzymatic activity in a de novo beta-barrel scaffold. Protein Sci., 31, 2022
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
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
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

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