7SQ5
 
 | | Designed trefoil knot protein, variant 3 | | Descriptor: | Designed trefoil knot protein, variant 3, SODIUM ION | | Authors: | Takushi, B, Doyle, L, Stoddard, B.L, Bradley, P. | | Deposit date: | 2021-11-04 | | Release date: | 2022-11-09 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.205 Å) | | Cite: | De novo design of knotted tandem repeat proteins.
Nat Commun, 14, 2023
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6CZI
 | | Structure of a redesigned beta barrel, mFAP1, bound to DFHBI | | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one, mFAP1 | | Authors: | Doyle, L.A, Stoddard, B.L. | | Deposit date: | 2018-04-09 | | Release date: | 2018-09-19 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | De novo design of a fluorescence-activating beta-barrel.
Nature, 561, 2018
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8EIL
 | | C-Terminal Domain of BrxL from Acinetobacter BREX type I phage restriction system | | Descriptor: | MALONIC ACID, Protease Lon-related BREX system protein BrxL, SUCCINIC ACID | | Authors: | Doyle, L.A, Stoddard, B.L, Kaiser, B. | | Deposit date: | 2022-09-15 | | Release date: | 2023-02-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor.
Nucleic Acids Res., 51, 2023
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6CZH
 | | Structure of a redesigned beta barrel, mFAP0, bound to DFHBI | | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one, mFAP0 | | Authors: | Doyle, L.A, Stoddard, B.L. | | Deposit date: | 2018-04-09 | | Release date: | 2018-09-19 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | De novo design of a fluorescence-activating beta-barrel.
Nature, 561, 2018
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6D0T
 | | De novo design of a fluorescence-activating beta barrel - BB1 | | Descriptor: | BB1 | | Authors: | Dou, J, Vorobieva, A.A, Sheffler, W, Doyle, L.A, Park, H, Bick, M.J, Mao, B, Foight, G.W, Lee, M, Carter, L, Sankaran, B, Ovchinnikov, S, Marcos, E, Huang, P, Vaughan, J.C, Stoddard, B.L, Baker, D. | | Deposit date: | 2018-04-10 | | Release date: | 2018-09-19 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.63 Å) | | Cite: | De novo design of a fluorescence-activating beta-barrel.
Nature, 561, 2018
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6CZG
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6CZJ
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5TGX
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8FLX
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5BYO
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299D
 | | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: THE HAMMERHEAD RIBOZYME | | Descriptor: | RNA HAMMERHEAD RIBOZYME | | Authors: | Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A. | | Deposit date: | 1996-12-14 | | Release date: | 1997-01-24 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
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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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8EMC
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8EMH
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5TGQ
 | | Restriction-modification system Type II R.SwaI, DNA free | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, CALCIUM ION, ... | | Authors: | Shen, B.W, stoddard, B.L. | | Deposit date: | 2016-09-28 | | Release date: | 2016-12-21 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (1.88 Å) | | Cite: | DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.
Nucleic Acids Res., 45, 2017
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4YHX
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4Z20
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4YIT
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301D
 | | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: RNA HAMMERHEAD RIBOZYME, MG(II)-SOAKED | | Descriptor: | MAGNESIUM ION, RNA HAMMERHEAD RIBOZYME | | Authors: | Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A. | | Deposit date: | 1996-12-14 | | Release date: | 1997-01-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
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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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300D
 | | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: RNA HAMMERHEAD RIBOZYME, MN(II)-SOAKED | | Descriptor: | MANGANESE (II) ION, RNA HAMMERHEAD RIBOZYME | | Authors: | Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A. | | Deposit date: | 1996-12-14 | | Release date: | 1997-01-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
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7UNH
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7UNI
 | | De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM | | Descriptor: | 1,2-ETHANEDIOL, PHOSPHATE ION, SP2-ZnPPaM designed chlorophyll dimer protein, ... | | Authors: | Kennedy, M.A, Stoddard, B.L, Ennist, N.M. | | Deposit date: | 2022-04-11 | | Release date: | 2023-04-19 | | Last modified: | 2024-06-12 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
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5ESP
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7UNJ
 | | De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester matching geometry of purple bacterial special pair, SP1-ZnPPaM | | Descriptor: | 1,2-ETHANEDIOL, SP1-ZnPPaM designed chlorophyll dimer protein, SULFATE ION, ... | | Authors: | Kennedy, M.A, Stoddard, B.L, Ennist, N.M. | | Deposit date: | 2022-04-11 | | Release date: | 2023-04-19 | | Last modified: | 2024-06-12 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
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