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3UD6
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BU of 3ud6 by Molmil
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
8T5E
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BU of 8t5e by Molmil
De novo design of high-affinity protein binders to bioactive helical peptides
Descriptor: Bcl-2-like protein 11, Bim_fulldiff
Authors:Torres, S.V, Leung, P.J.Y, Bera, A.K, Baker, D, Kang, A.
Deposit date:2023-06-13
Release date:2024-01-10
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (3 Å)
Cite:De novo design of high-affinity binders of bioactive helical peptides.
Nature, 626, 2024
8T5F
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BU of 8t5f by Molmil
De novo design of high-affinity protein binders to bioactive helical peptides
Descriptor: Parathyroid hormone
Authors:Torres, S.V, Leung, P.J.Y, Bera, A.K, Baker, D, Kang, A.
Deposit date:2023-06-13
Release date:2024-01-10
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:De novo design of high-affinity binders of bioactive helical peptides.
Nature, 626, 2024
8VC8
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BU of 8vc8 by Molmil
Crystal structure of heme-loaded design: HEM_3.C9
Descriptor: HEM_3.C9, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION
Authors:Kalvet, I, Bera, A.K, Baker, D.
Deposit date:2023-12-13
Release date:2024-03-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Generalized biomolecular modeling and design with RoseTTAFold All-Atom.
Science, 2024
8GLT
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BU of 8glt by Molmil
Backbone model of de novo-designed chlorophyll-binding nanocage O32-15
Descriptor: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model, C3-comp_O32-15
Authors:Redler, R.L, Ennist, N.M, Wang, S, Baker, D, Ekiert, D.C, Bhabha, G.
Deposit date:2023-03-23
Release date:2024-03-27
Method:ELECTRON MICROSCOPY (6.5 Å)
Cite:De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs
To Be Published
8TCG
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BU of 8tcg by Molmil
Integrin alpha-v beta-6 in complex with minibinder B6_BP_dslf
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Integrin alpha-V heavy chain, ...
Authors:Campbell, M.G, Fernandez, A, Roy, A, Kraft, J, Baker, D.
Deposit date:2023-06-30
Release date:2023-09-27
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:De novo design of highly selective miniprotein inhibitors of integrins alpha v beta 6 and alpha v beta 8.
Nat Commun, 14, 2023
8TCF
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BU of 8tcf by Molmil
Integrin alpha-v beta-8 in complex with minibinder B8_BP_dsulf
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ...
Authors:Campbell, M.G, Fernandez, A, Roy, A, Kraft, J, Baker, D.
Deposit date:2023-06-30
Release date:2023-09-27
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:De novo design of highly selective miniprotein inhibitors of integrins alpha v beta 6 and alpha v beta 8.
Nat Commun, 14, 2023
8UGC
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BU of 8ugc by Molmil
FD15: Flat repeat helix-turn-helix-turn protein
Descriptor: FD15
Authors:Davila-Hernandez, F, Bera, A.K, Kang, A, Baker, D.
Deposit date:2023-10-05
Release date:2023-12-27
Method:X-RAY DIFFRACTION (4 Å)
Cite:Directing polymorph specific calcium carbonate formation with de novo protein templates.
Nat Commun, 14, 2023
8U5A
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BU of 8u5a by Molmil
Improving protein expression, stability, and function with ProteinMPNN
Descriptor: Designed myoglobin, PROTOPORPHYRIN IX CONTAINING FE
Authors:Kalvet, I, Bera, A.K, Baker, D.
Deposit date:2023-09-12
Release date:2024-01-17
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2 Å)
Cite:Improving Protein Expression, Stability, and Function with ProteinMPNN.
J.Am.Chem.Soc., 146, 2024
8G9J
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BU of 8g9j by Molmil
Geometrically programmable nanomaterial construction using regularized protein building blocks
Descriptor: THR1
Authors:Huddy, T, Bera, A.K, Baker, D.
Deposit date:2023-02-21
Release date:2024-03-13
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Blueprinting extendable nanomaterials with standardized protein blocks.
Nature, 2024
8G9K
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BU of 8g9k by Molmil
Geometrically programmable nanomaterial construction using regularized protein building blocks
Descriptor: THR2
Authors:Bera, A.K, Huddy, T, Baker, D, Kang, A.
Deposit date:2023-02-21
Release date:2024-03-13
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.48 Å)
Cite:Blueprinting extendable nanomaterials with standardized protein blocks.
Nature, 2024
8GA6
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BU of 8ga6 by Molmil
Geometrically programmable nanomaterial construction using regularized protein building blocks
Descriptor: THR6
Authors:Huddy, T, Bera, A.K, Baker, D, Kang, A.
Deposit date:2023-02-22
Release date:2024-03-13
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Blueprinting extendable nanomaterials with standardized protein blocks.
Nature, 2024
8GA7
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BU of 8ga7 by Molmil
Geometrically programmable nanomaterial construction using regularized protein building blocks
Descriptor: THR5
Authors:Huddy, T, Bera, A.K, Baker, D, Kang, A.
Deposit date:2023-02-22
Release date:2024-03-13
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.93 Å)
Cite:Blueprinting extendable nanomaterials with standardized protein blocks.
Nature, 2024
8E55
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BU of 8e55 by Molmil
Design of Diverse Asymmetric Pockets in de novo Homo-oligomeric Proteins
Descriptor: SG135
Authors:Gerben, S, Borst, A.J, Baker, D.
Deposit date:2022-08-19
Release date:2023-01-25
Method:ELECTRON MICROSCOPY (3.85 Å)
Cite:Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.
Biochemistry, 62, 2023
8E1E
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BU of 8e1e by Molmil
Scaffolding protein functional sites using deep learning
Descriptor: SG122_C3
Authors:Bera, A.K, Gerben, S, Baker, D.
Deposit date:2022-08-10
Release date:2023-08-16
Method:X-RAY DIFFRACTION (4.27 Å)
Cite:Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.
Biochemistry, 62, 2023
7UR7
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BU of 7ur7 by Molmil
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
Method:X-RAY DIFFRACTION (1.21 Å)
Cite:De novo design of small beta barrel proteins.
Proc.Natl.Acad.Sci.USA, 120, 2023
7UR8
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BU of 7ur8 by Molmil
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
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:De novo design of small beta barrel proteins.
Proc.Natl.Acad.Sci.USA, 120, 2023
8F4X
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BU of 8f4x by Molmil
Top-down design of protein architectures with reinforcement learning
Descriptor: RC_I_1-H11
Authors:Borst, A.J, Baker, D.
Deposit date:2022-11-11
Release date:2023-05-10
Method:ELECTRON MICROSCOPY (3.01 Å)
Cite:Top-down design of protein architectures with reinforcement learning.
Science, 380, 2023
8F53
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BU of 8f53 by Molmil
Top-down design of protein architectures with reinforcement learning
Descriptor: RC_I_2
Authors:Borst, A.J, Baker, D.
Deposit date:2022-11-11
Release date:2023-05-10
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Top-down design of protein architectures with reinforcement learning.
Science, 380, 2023
8F54
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BU of 8f54 by Molmil
Top-down design of protein architectures with reinforcement learning
Descriptor: RC_I_1
Authors:Borst, A.J, Baker, D.
Deposit date:2022-11-11
Release date:2023-05-10
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Top-down design of protein architectures with reinforcement learning.
Science, 380, 2023
8FIT
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BU of 8fit by Molmil
Multi-state design of two-state switchable hinge proteins
Descriptor: cs074A
Authors:Bera, A.K, Praetorius, F, Baker, D.
Deposit date:2022-12-16
Release date:2023-08-16
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Design of stimulus-responsive two-state hinge proteins.
Science, 381, 2023
8FIN
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BU of 8fin by Molmil
Multi-state design of two-state switchable hinge proteins
Descriptor: cs207A
Authors:Bera, A.K, Leung, P.J.Y, Baker, D.
Deposit date:2022-12-16
Release date:2023-08-16
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Design of stimulus-responsive two-state hinge proteins.
Science, 381, 2023
8FIQ
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BU of 8fiq by Molmil
Multi-state design of two-state switchable hinge proteins
Descriptor: cs207AB
Authors:Bera, A.K, Leung, P.J.Y, Baker, D.
Deposit date:2022-12-16
Release date:2023-08-16
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.66 Å)
Cite:Design of stimulus-responsive two-state hinge proteins.
Science, 381, 2023
8FIH
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BU of 8fih by Molmil
Multi-state design of two-state switchable hinge proteins
Descriptor: 3hb05, PHOSPHATE ION
Authors:Bera, A.K, Broerman, A, Baker, D.
Deposit date:2022-12-16
Release date:2023-08-16
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Design of stimulus-responsive two-state hinge proteins.
Science, 381, 2023
8FJF
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BU of 8fjf by Molmil
The three-repeat design H10
Descriptor: H10
Authors:Bera, A.K, An, L, Baker, D.
Deposit date:2022-12-19
Release date:2023-09-27
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Hallucination of closed repeat proteins containing central pockets.
Nat.Struct.Mol.Biol., 30, 2023

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PDB entries from 2024-03-27

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