1NX1
 
 | | Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (DIC) | | Descriptor: | CALCIUM ION, Calcium-dependent protease, small subunit, ... | | Authors: | Todd, B, Moore, D, Deivanayagam, C.C.S, Lin, G.-D, Chattopadhyay, D, Maki, M, Wang, K.K.W, Narayana, S.V.L. | | Deposit date: | 2003-02-07 | | Release date: | 2003-08-19 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
J.Mol.Biol., 328, 2003
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1NX2
 | | Calpain Domain VI | | Descriptor: | CALCIUM ION, Calcium-dependent protease, small subunit | | Authors: | Todd, B, Moore, D, Deivanayagam, C.C.S, Lin, G.-D, Chattopadhyay, D, Maki, M, Wang, K.K.W, Narayana, S.V.L. | | Deposit date: | 2003-02-07 | | Release date: | 2003-08-19 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
J.Mol.Biol., 328, 2003
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1NX0
 | | Structure of Calpain Domain 6 in Complex with Calpastatin DIC | | Descriptor: | CALCIUM ION, Calcium-dependent protease, small subunit, ... | | Authors: | Todd, B, Moore, D, Deivanayagam, C.C.S, Lin, G.-D, Chattopadhyay, D, Maki, M, Wang, K.K.W, Narayana, S.V.L. | | Deposit date: | 2003-02-07 | | Release date: | 2003-08-19 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
J.Mol.Biol., 328, 2003
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1NX3
 | | Calpain Domain VI in Complex with the Inhibitor PD150606 | | Descriptor: | 3-(4-IODO-PHENYL)-2-MERCAPTO-PROPIONIC ACID, CALCIUM ION, Calcium-dependent protease, ... | | Authors: | Todd, B, Moore, D, Deivanayagam, C.C.S, Lin, G.-D, Chattopadhyay, D, Maki, M, Wang, K.K.W, Narayana, S.V.L. | | Deposit date: | 2003-02-07 | | Release date: | 2003-08-19 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
J.Mol.Biol., 328, 2003
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1D4L
 | | HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR | | Descriptor: | (10S,13S,1'R)-13-[1'-HYDROXY-2'-(N-P-AMINOBENZENESULFONYL-1''-AMINO-3''-METHYLBUTYL)ETHYL]-8,11-DIOXO-10-ISOPROPYL-2-OXA-9,12-DIAZABICYCLO [13.2.2]NONADECA-15,17,18-TRIENE, HIV-1 PROTEASE, SULFATE ION | | Authors: | Tyndall, J.D, Reid, R.C, Tyssen, D.P, Jardine, D.K, Todd, B, Passmore, M, March, D.R, Pattenden, L.K, Alewood, D, Hu, S.H, Alewood, P.F, Birch, C.J, Martin, J.L, Fairlie, D.P. | | Deposit date: | 1999-10-04 | | Release date: | 2000-10-11 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.
J.Med.Chem., 43, 2000
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1D4K
 | | HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR | | Descriptor: | HIV-1 PROTEASE, N-13-[(10S,13S)-9,12-DIOXO-10-(2-BUTYL)-2-OXA-8,11-DIAZABICYCLO [13.2.2] NONADECA-15,17,18-TRIENE] (2R)-BENZYL-(4S)-HYDROXY-5-AMINOPENTANOIC (1R)-HYDROXY-(2S)-INDANEAMIDE, SULFATE ION | | Authors: | Tyndall, J.D, Reid, R.C, Tyssen, D.P, Jardine, D.K, Todd, B, Passmore, M, March, D.R, Pattenden, L.K, Alewood, D, Hu, S.H, Alewood, P.F, Birch, C.J, Martin, J.L, Fairlie, D.P. | | Deposit date: | 1999-10-04 | | Release date: | 2000-10-11 | | Last modified: | 2021-11-03 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.
J.Med.Chem., 43, 2000
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4LQ0
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4LOX
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3G77
 | | Bacterial cytosine deaminase V152A/F316C/D317G mutant | | Descriptor: | Cytosine deaminase, FE (III) ION | | Authors: | Stoddard, B, Zhao, L. | | Deposit date: | 2009-02-09 | | Release date: | 2009-09-22 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo.
Cancer Res., 69, 2009
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3DF0
 | | Calcium-dependent complex between m-calpain and calpastatin | | Descriptor: | CALCIUM ION, Calpain small subunit 1, Calpain-2 catalytic subunit, ... | | Authors: | Moldoveanu, T, Gehring, K, Green, D.R. | | Deposit date: | 2008-06-11 | | Release date: | 2008-11-11 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.
Nature, 456, 2008
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3O6Y
 | | Robust computational design, optimization, and structural characterization of retroaldol enzymes | | Descriptor: | Retro-Aldolase, SULFATE ION | | Authors: | Althoff, E.A, Wang, L, Jiang, L, Moody, J, Bolduc, J, Lassila, J.K, Wang, Z.Z, Smith, M, Hari, S, Herschlag, D, Stoddard, B.L, Baker, D. | | Deposit date: | 2010-07-29 | | Release date: | 2011-06-29 | | Last modified: | 2023-09-06 | | 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
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3NXF
 | | Robust computational design, optimization, and structural characterization of retroaldol enzymes | | Descriptor: | Retro-Aldolase, SULFATE ION | | Authors: | Althoff, E.A, Jiang, L, Wang, L, Lassila, J.K, Moody, J, Bolduc, J, Wang, Z.Z, Smith, M, Hari, S, Herschlag, D, Stoddard, B.L, Baker, D. | | Deposit date: | 2010-07-13 | | Release date: | 2011-06-29 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
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7RKC
 | | Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633 | | Descriptor: | ACETATE ION, D_3_633 | | Authors: | Kennedy, M.A, Stoddard, B.L, Hicks, D.R, Bera, A.K. | | Deposit date: | 2021-07-22 | | Release date: | 2022-05-18 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | De novo design of protein homodimers containing tunable symmetric protein pockets.
Proc.Natl.Acad.Sci.USA, 119, 2022
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5E63
 | | K262A mutant of I-SmaMI | | Descriptor: | 2-(2-METHOXYETHOXY)ETHANOL, 2-METHOXYETHANOL, DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3'), ... | | Authors: | Shen, B, Stoddard, B. | | Deposit date: | 2015-10-09 | | Release date: | 2016-01-13 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.
J.Mol.Biol., 428, 2016
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3UVF
 | | Expanding LAGALIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space | | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, Intron-encoded DNA endonuclease I-HjeMI, ... | | Authors: | Jacoby, K, Metzger, M, Shen, B, Jarjour, J, Stoddard, B, Scharenberg, A. | | Deposit date: | 2011-11-29 | | Release date: | 2012-02-29 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.
Nucleic Acids Res., 40, 2012
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7T8K
 | | BrxR from Acinetobacter BREX type I phage restriction system bound to DNA | | Descriptor: | 1,2-ETHANEDIOL, BrxR, CHLORIDE ION, ... | | Authors: | Doyle, L, Kaiser, B, Stoddard, B. | | Deposit date: | 2021-12-16 | | Release date: | 2022-05-18 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system.
Nucleic Acids Res., 50, 2022
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7T8L
 | | BrxR from Acinetobacter BREX type I phage restriction system | | Descriptor: | 1,2-ETHANEDIOL, BrxR, CHLORIDE ION | | Authors: | Doyle, L, Kaiser, B, Stoddard, B. | | Deposit date: | 2021-12-16 | | Release date: | 2022-05-18 | | Last modified: | 2022-06-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system.
Nucleic Acids Res., 50, 2022
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5IEN
 | | Structure of CDL2.2, a computationally designed Vitamin-D3 binder | | Descriptor: | 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL, CDL2.2, GLYCEROL | | Authors: | Stoddard, B.L, Doyle, L.A. | | Deposit date: | 2016-02-25 | | Release date: | 2017-03-01 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.089 Å) | | Cite: | Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.
Protein Eng.Des.Sel., 31, 2018
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5IEO
 | | Structure of CDL2.3a, a computationally designed Vitamin-D3 binder | | Descriptor: | 1,2-ETHANEDIOL, 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL, CDL2.3a | | Authors: | Stoddard, B.L, Doyle, L.A. | | Deposit date: | 2016-02-25 | | Release date: | 2017-03-01 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.851 Å) | | Cite: | Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.
Protein Eng.Des.Sel., 31, 2018
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5IEP
 | | Structure of CDL2.3b, a computationally designed Vitamin-D3 binder | | Descriptor: | 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL, CDL2.3b | | Authors: | Stoddard, B.L, Doyle, L.A. | | Deposit date: | 2016-02-25 | | Release date: | 2017-03-01 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.893 Å) | | Cite: | Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.
Protein Eng.Des.Sel., 31, 2018
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3UD6
 | | 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: | 2023-09-13 | | 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
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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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7RMY
 | | De Novo designed tunable protein pockets, D_3-337 | | Descriptor: | De Novo designed tunable homodimer, D_3-337 | | Authors: | Bera, A.K, Hicks, D.R, Kang, A, Sankaran, B, Baker, D. | | Deposit date: | 2021-07-28 | | Release date: | 2022-08-03 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (3.17 Å) | | Cite: | De novo design of protein homodimers containing tunable symmetric protein pockets.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RMX
 | | Structure of De Novo designed tunable symmetric protein pockets | | Descriptor: | Tunable symmetric protein, D_3_212 | | Authors: | Bera, A.K, Hicks, D.R, Kang, A, Sankaran, B, Baker, D. | | Deposit date: | 2021-07-28 | | Release date: | 2022-08-03 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | De novo design of protein homodimers containing tunable symmetric protein pockets.
Proc.Natl.Acad.Sci.USA, 119, 2022
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5CW9
 | | Crystal structure of De novo designed ferredoxin-ferredoxin domain insertion protein | | Descriptor: | De novo designed ferredoxin-ferredoxin domain insertion protein | | Authors: | DiMaio, F, King, I.C, Gleixner, J, Doyle, L, Stoddard, B, Baker, D. | | Deposit date: | 2015-07-28 | | Release date: | 2015-09-23 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (3.108 Å) | | Cite: | Precise assembly of complex beta sheet topologies from de novo designed building blocks.
Elife, 4, 2015
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