PDB: 5689 resultsInfo pagesStatus searchChemie searchBIRD

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6UU3	E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Old" crystal soaked with GTP, ATP, CTP, and ddTTP for 30 minutes) Descriptor: CYTIDINE-5'-TRIPHOSPHATE, 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: 2024-11-06 Method: X-RAY DIFFRACTION (4.002 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU6	E. coli sigma-S transcription initiation complex with a 4-nt RNA and a UTP ("Old" crystal soaked with UTP, ddCTP, and dinucleotide ApG for 30 minutes) 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 (4.201 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU1	E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Fresh" crystal soaked with CTP, GTP, and ddTTP for 30 minutes) Descriptor: CYTIDINE-5'-TRIPHOSPHATE, 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 (4.097 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UTY	E. coli sigma-S transcription initiation complex with a mismatching CTP ("Old" crystal soaked with CTP for 30 minutes) Descriptor: CYTIDINE-5'-TRIPHOSPHATE, 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 (4.15 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UTZ	E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP and UTP 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 (3.803 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UTX	E. coli sigma-S transcription initiation complex with an empty bubble ("Old" crystal) 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 (4.05 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UUB	E. coli sigma-S transcription initiation complex with a mismatching UTP ("Fresh" crystal soaked with UTP for 2 hours) 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 (3.955 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU2	E. coli sigma-S transcription initiation complex with 3-nt RNA ("Old" crystal soaked with GTP and ATP for 30 minutes) 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 (4.404 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU9	E. coli mutant sigma-S transcription initiation complex with an 8-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, CTP, and ddATP for 30 minutes) Descriptor: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE, DIPHOSPHATE, DNA-directed RNA polymerase subunit alpha, ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2024-10-23 Method: X-RAY DIFFRACTION (5.4 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU4	E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes) 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 (4.305 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UUC	E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching ATP ("Fresh" crystal soaked with ATP for 2 hours) Descriptor: ADENOSINE-5'-TRIPHOSPHATE, 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 (4.096 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU7	E. coli sigma-S transcription initiation complex with a 6-nt RNA and an NTP ("Old" crystal soaked with UTP, CTP, ddGTP, and dinucleotide ApG for 30 minutes) Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, 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: 2024-11-06 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
6UU5	E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Old" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA 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 (5.403 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
4FIC	Kinase domain of cSrc in complex with a hinge region-binding fragment Descriptor: 6-phenyl[1,2,4]triazolo[1,5-a]pyrazin-2-amine, Proto-oncogene tyrosine-protein kinase Src Authors: Richters, A, Rauh, D. Deposit date: 2012-06-08 Release date: 2013-04-10 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.5 Å) Cite: De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments. Acs Chem.Biol., 8, 2013
6TWC	Crystal Structure of the Catalytic Domain of the Coagulation Factor XIa in Complex with Double Bridged Peptide F21 Descriptor: ACETONE, Coagulation factor XI, Double Bridged Peptide F21 Authors: Kong, X.D, Pojer, F, Heinis, C. Deposit date: 2020-01-13 Release date: 2020-05-20 Last modified: 2024-01-24 Method: X-RAY DIFFRACTION (2.86 Å) Cite: De novo development of proteolytically resistant therapeutic peptides for oral administration. Nat Biomed Eng, 4, 2020
6TWB	Crystal Structure of the Catalytic Domain of Coagulation Factor XIa in Complex with Double Bridged Peptide F19 Descriptor: AMMONIUM ION, Coagulation factor XI, Double Bridged Peptide F19 Authors: Kong, X.D, Pojer, F, Heinis, C. Deposit date: 2020-01-13 Release date: 2020-05-13 Last modified: 2024-01-24 Method: X-RAY DIFFRACTION (2.91 Å) Cite: De novo development of proteolytically resistant therapeutic peptides for oral administration. Nat Biomed Eng, 4, 2020
4N5R	Hen egg-white lysozyme phased using free-electron laser data Descriptor: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID, GADOLINIUM ATOM, Lysozyme C Authors: Barends, T.R.M, Foucar, L, Botha, S, Doak, R.B, Shoeman, R.L, Nass, K, Koglin, J.E, Williams, G.J, Boutet, S, Messerschmidt, M, Schlichting, I. Deposit date: 2013-10-10 Release date: 2013-11-27 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (2.1 Å) Cite: De novo protein crystal structure determination from X-ray free-electron laser data. Nature, 505, 2014
6E9R	DHF46 filament Descriptor: DHF46 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 (5.9 Å) Cite: De novo design of self-assembling helical protein filaments. Science, 362, 2018
6E9Z	DHF119 filament Descriptor: DHF119 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 (3.4 Å) Cite: De novo design of self-assembling helical protein filaments. Science, 362, 2018
6E9V	DHF79 filament Descriptor: DHF79 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 (6.9 Å) Cite: De novo design of self-assembling helical protein filaments. Science, 362, 2018
6VFK	De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface Descriptor: BG505-SOSIP-T33_dn10A, T33_dn10B Authors: Antanasijevic, A, Ward, A.B. Deposit date: 2020-01-05 Release date: 2020-07-22 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (4.25 Å) Cite: Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens. Plos Pathog., 16, 2020
6O35	Crystal structure of a de novo designed octameric helical-bundle protein Descriptor: de novo designed WSHC8 Authors: Bick, M.J, Xu, C, Sankaran, B, Baker, D. Deposit date: 2019-02-25 Release date: 2020-03-18 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Computational design of transmembrane pores. Nature, 585, 2020
1JM0	CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL Descriptor: DIMETHYL SULFOXIDE, MANGANESE (II) ION, PROTEIN (FOUR-HELIX BUNDLE MODEL) Authors: Di Costanzo, L, Geremia, S. Deposit date: 2001-07-17 Release date: 2002-01-16 Last modified: 2024-10-30 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center. J.Am.Chem.Soc., 123, 2001
1JMB	CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL Descriptor: DIMETHYL SULFOXIDE, MANGANESE (II) ION, PROTEIN (FOUR-HELIX BUNDLE MODEL) Authors: Di Costanzo, L, Geremia, S. Deposit date: 2001-07-18 Release date: 2002-01-16 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center. J.Am.Chem.Soc., 123, 2001
9EXK	Scalable protein design using hallucination in a relaxed sequence space Descriptor: De novo designed protein K12 Authors: Frank, C.J, Dietz, H. Deposit date: 2024-04-08 Release date: 2024-10-16 Last modified: 2024-11-06 Method: ELECTRON MICROSCOPY (3.36 Å) Cite: Scalable protein design using optimization in a relaxed sequence space. Science, 386, 2024

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