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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
Last modified:	2024-05-01
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science, 384, 2024

8FBO

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Descriptor:	KWOCA_102
Authors:	Wang, J.Y, Khmelinskaia, A, Bera, A.K, King, N.P.
Deposit date:	2022-11-29
Release date:	2023-03-22
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (3.4 Å)
Cite:	Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc.Natl.Acad.Sci.USA, 120, 2023

8FBJ

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Descriptor:	KWOCA_60
Authors:	Wang, J.Y, Khmelinskaia, A, Bera, A.K, King, N.P.
Deposit date:	2022-11-29
Release date:	2023-03-22
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (3.25 Å)
Cite:	Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc.Natl.Acad.Sci.USA, 120, 2023

8FBI

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Descriptor:	KWOCA_39
Authors:	Wang, J.Y, Khmelinskaia, A, Bera, A.K, King, N.P.
Deposit date:	2022-11-29
Release date:	2023-03-22
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (3.61 Å)
Cite:	Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc.Natl.Acad.Sci.USA, 120, 2023

8FBK

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Descriptor:	KWOCA_65
Authors:	Wang, J.Y, Khmelinskaia, A, Bera, A.K, King, N.P.
Deposit date:	2022-11-29
Release date:	2023-03-22
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (3.15 Å)
Cite:	Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc.Natl.Acad.Sci.USA, 120, 2023

8FBN

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Descriptor:	KWOCA_73
Authors:	Wang, J.Y, Khmelinskaia, A, Bera, A.K, King, N.P.
Deposit date:	2022-11-29
Release date:	2023-03-22
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (3.04 Å)
Cite:	Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc.Natl.Acad.Sci.USA, 120, 2023

7UWZ

NMR solution structure of the De novo designed small beta-barrel protein 33_bp_sh3
Descriptor:	De novo designed small beta-barrel protein 33_bp_sh3
Authors:	Peterson, F.C, Kim, D.E, Jensen, D.R, Saleem, A, Chow, C.M, Volkman, B.F, Baker, D.
Deposit date:	2022-05-04
Release date:	2023-03-22
Last modified:	2024-05-15
Method:	SOLUTION NMR
Cite:	De novo design of small beta barrel proteins. Proc.Natl.Acad.Sci.USA, 120, 2023

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

9DEC

Crystal Structure of D9-threaded
Descriptor:	D9-threaded
Authors:	Bera, A.K, Sims, J, Baker, D.
Deposit date:	2024-08-28
Release date:	2025-03-26
Method:	X-RAY DIFFRACTION (2.04 Å)
Cite:	Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding. Biorxiv, 2025

9DE9

Crystal Structure of HE-B11
Descriptor:	HE-B11
Authors:	Bera, A.K, Sims, J, Baker, D.
Deposit date:	2024-08-28
Release date:	2025-03-26
Method:	X-RAY DIFFRACTION (2.52 Å)
Cite:	Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding. Biorxiv, 2025

9DEA

Crystal Structure of C3-threaded
Descriptor:	C3_threaded
Authors:	Bera, A.K, Sims, J, Baker, D.
Deposit date:	2024-08-28
Release date:	2025-03-26
Method:	X-RAY DIFFRACTION (2.87 Å)
Cite:	Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding. Biorxiv, 2025

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

7UNH

De novo designed chlorophyll dimer protein in apo state, SP2
Descriptor:	1,2-ETHANEDIOL, SP2 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 (2.4 Å)
Cite:	De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat.Chem.Biol., 2024

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

8EVM

De novo design of chlorophyll special pair containing protein assemblies
Descriptor:	Chlorophyll dimer protein designs, Special Pair 3 (SP3x)
Authors:	Bera, A.K, Ennist, N.M.
Deposit date:	2022-10-20
Release date:	2024-05-15
Last modified:	2024-07-10
Method:	X-RAY DIFFRACTION (3.05 Å)
Cite:	De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat.Chem.Biol., 20, 2024

8VL3

Solution NMR structure of de novo designed protein F3 parent
Descriptor:	De novo designed protein F3 parent
Authors:	McShan, A.C, Simma, M.K.
Deposit date:	2024-01-11
Release date:	2024-08-07
Last modified:	2024-12-04
Method:	SOLUTION NMR
Cite:	Multistate and functional protein design using RoseTTAFold sequence space diffusion. Nat.Biotechnol., 2024

8VL4

Solution NMR Structure of de novo design protein 312 parent
Descriptor:	De novo design protein 312 parent
Authors:	McShan, A.C, Simma, M.K.
Deposit date:	2024-01-11
Release date:	2024-08-07
Last modified:	2024-12-04
Method:	SOLUTION NMR
Cite:	Multistate and functional protein design using RoseTTAFold sequence space diffusion. Nat.Biotechnol., 2024

9FDG

Solution structure of a de novo designed 12-stranded transmembrane beta-barrel in LDAO micelles.
Descriptor:	TMB12sol9_3
Authors:	Muentener, T, Hiller, S.
Deposit date:	2024-05-17
Release date:	2024-10-16
Method:	SOLUTION NMR
Cite:	Sculpting conducting nanopore size and shape through de novo protein design. Science, 385, 2024

7K3H

Crystal structure of deep network hallucinated protein 0217
Descriptor:	Network hallucinated protein 0217
Authors:	Pellock, S.J, Anishchenko, I, Chidyausiku, T.M, Bera, A.K, DiMaio, F, Baker, D.
Deposit date:	2020-09-11
Release date:	2021-12-22
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	De novo protein design by deep network hallucination. Nature, 600, 2021

8E55

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
Last modified:	2025-05-21
Method:	ELECTRON MICROSCOPY (3.85 Å)
Cite:	Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins. Biochemistry, 62, 2023

8E1E

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

8EOV

Precisely patterned nanofibers made from extendable protein multiplexes
Descriptor:	C2HR1_4r, PHOSPHATE ION
Authors:	Bera, A.K, Bethel, N.P.
Deposit date:	2022-10-04
Release date:	2023-08-16
Last modified:	2023-12-20
Method:	X-RAY DIFFRACTION (1.59 Å)
Cite:	Precisely patterned nanofibres made from extendable protein multiplexes. Nat.Chem., 15, 2023

8EOX

Precisely patterned nanofibers made from extendable protein multiplexes
Descriptor:	C4HR1_4r
Authors:	Bera, A.K, Bethel, N.P.
Deposit date:	2022-10-04
Release date:	2023-08-16
Last modified:	2023-12-20
Method:	X-RAY DIFFRACTION (3.3 Å)
Cite:	Precisely patterned nanofibres made from extendable protein multiplexes. Nat.Chem., 15, 2023

8EK4

De novo designed ice-binding proteins from twist-constrained helices
Descriptor:	Ice-binding protein TIP-99a
Authors:	Bera, A.K, De Haas, R.J.
Deposit date:	2022-09-19
Release date:	2023-07-12
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.35 Å)
Cite:	De novo designed ice-binding proteins from twist-constrained helices. Proc.Natl.Acad.Sci.USA, 120, 2023

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