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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Bradley, P."

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	synthetic construct (12)
	Xanthomonas oryzae pv. oryzae PXO99A (1)

Taxonomy

	other sequences (12)
	Bacteria (1)

Experimental Method

X-RAY DIFFRACTION (13)

Polymer Entity Type

	Protein (13)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (1)
	2.0 - 2.5 (6)
	2.5 - 3.0 (2)
	3.0 - 3.5 (3)

Release Date

	2010 - 2014 (1)
	2015 - 2019 (6)
	2020 - 2024 (6)

Symmetry Type

	Asymmetric (10)
	Cyclic (3)

SCOP Classification

All alpha proteins (1)

AllSelected

1 to 13 of 13 Structures

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3UGM \| pdb_00003ugm	Download File View File

Structure of TAL effector PthXo1 bound to its DNA target

Mak, A.N.S., Bradley, P., Cernadas, R.A., Bogdanove, A.J., Stoddard, B.L.

(2012) Science 335: 716-719

Released	2012-01-04
Method	X-RAY DIFFRACTION 3 Å
Organisms	Xanthomonas oryzae pv. oryzae PXO99A
Macromolecule	TAL effector AvrBs3/PthA (protein) DNA-1 (nucleic acid) DNA-2 (nucleic acid)

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4YXX \| pdb_00004yxx	Download File View File

Computationally designed left-handed alpha/alpha toroid with 6 repeats

Doyle, L., Bolduc, J., Stoddard, B.L., Bradley, P.

(2015) Nature 528: 585-588

Released	2015-12-16
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	synthetic construct
Macromolecule	dTor_6x35L (protein)

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4YXY \| pdb_00004yxy	Download File View File

Computationally designed left-handed alpha/alpha toroid with 9 repeats; two linked rings of 12 repeats each structure

Doyle, L., Stoddard, B.L., Bradley, P.

(2015) Nature 528: 585-588

Released	2015-12-16
Method	X-RAY DIFFRACTION 3.203 Å
Organisms	synthetic construct
Macromolecule	dTor_9x31L (protein)

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4YXZ \| pdb_00004yxz	Download File View File

Computationally designed left-handed alpha/alpha toroid with 9 repeats

Doyle, L., Stoddard, B.L., Bradley, P.

(2015) Nature 528: 585-588

Released	2015-12-16
Method	X-RAY DIFFRACTION 2.496 Å
Organisms	synthetic construct
Macromolecule	dTor_9x31L (protein)

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4YY2 \| pdb_00004yy2	Download File View File

Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group P212121

Hallinan, J.P., Bradley, P., Stoddard, B.L.

(2015) Nature 528: 585-588

Released	2015-12-16
Method	X-RAY DIFFRACTION 1.854 Å
Organisms	synthetic construct
Macromolecule	dTor_3x33L (protein)
Unique Ligands	NA

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4YY5 \| pdb_00004yy5	Download File View File

Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group P43212

Hallinan, J.P., Bradley, P., Stoddard, B.L.

(2015) Nature 528: 585-588

Released	2015-12-16
Method	X-RAY DIFFRACTION 2.78 Å
Organisms	synthetic construct
Macromolecule	dTor_3x33L (protein)

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5BYO \| pdb_00005byo	Download File View File

Computationally designed left-handed alpha/alpha toroid with 12 repeats

Doyle, L., Stoddard, B.L., Bradley, P.

(2015) Nature 528: 585-588

Released	2015-12-16
Method	X-RAY DIFFRACTION 2.503 Å
Organisms	synthetic construct
Macromolecule	dTor_12x31L (protein)

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6XR1 \| pdb_00006xr1	Download File View File

Computationally designed right-handed alpha/alpha single-chain toroid with 9 repeats

Hallinan, J.P., Doyle, L., Bradley, P., Stoddard, B.L.

(2021) Commun Biol 4: 1240-1240

Released	2021-07-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	synthetic construct
Macromolecule	dTor_9x57R (protein)

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6XR2 \| pdb_00006xr2	Download File View File

Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit

Hallinan, J.P., Doyle, L., Bradley, P., Stoddard, B.L.

(2021) Commun Biol 4: 1240-1240

Released	2021-07-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	synthetic construct
Macromolecule	dTor_3x57R (protein)

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7SQ3 \| pdb_00007sq3	Download File View File

Designed trefoil knot protein, variant 1

Takushi, B., Doyle, L., Stoddard, B.L., Bradley, P.

(2023) Nat Commun 14: 6746-6746

Released	2022-06-29
Method	X-RAY DIFFRACTION 2.453 Å
Organisms	synthetic construct
Macromolecule	Designed trefoil knot protein, variant 1 (protein)
Unique Ligands	CL, NA

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7SQ4 \| pdb_00007sq4	Download File View File

Designed trefoil knot protein, variant 2

Takushi, B., Doyle, L., Stoddard, B.L., Bradley, P.

(2023) Nat Commun 14: 6746-6746

Released	2022-06-29
Method	X-RAY DIFFRACTION 1.493 Å
Organisms	synthetic construct
Macromolecule	Designed trefoil knot protein, variant 2 (protein)
Unique Ligands	MPD, NA

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7SQ5 \| pdb_00007sq5	Download File View File

Designed trefoil knot protein, variant 3

Takushi, B., Doyle, L., Stoddard, B.L., Bradley, P.

(2023) Nat Commun 14: 6746-6746

Released	2022-11-09
Method	X-RAY DIFFRACTION 2.205 Å
Organisms	synthetic construct
Macromolecule	Designed trefoil knot protein, variant 3 (protein)
Unique Ligands	NA

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8ETQ \| pdb_00008etq	Download File View File

Designed pentafoil knot protein folded into a trefoil knot

Doyle, L.A., Kibler, R.D., Bradley, P., Stoddard, B.L.

(2023) Nat Commun 14: 6746-6746

Released	2023-10-25
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	synthetic construct
Macromolecule	k-cTRP5 (protein)

1 to 13 of 13 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3UGM | pdb_00003ugm

Structure of TAL effector PthXo1 bound to its DNA target

4YXX | pdb_00004yxx

Computationally designed left-handed alpha/alpha toroid with 6 repeats

4YXY | pdb_00004yxy

Computationally designed left-handed alpha/alpha toroid with 9 repeats; two linked rings of 12 repeats each structure

4YXZ | pdb_00004yxz

Computationally designed left-handed alpha/alpha toroid with 9 repeats

4YY2 | pdb_00004yy2

Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group P212121

4YY5 | pdb_00004yy5

Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group P43212

5BYO | pdb_00005byo

Computationally designed left-handed alpha/alpha toroid with 12 repeats

6XR1 | pdb_00006xr1

Computationally designed right-handed alpha/alpha single-chain toroid with 9 repeats

6XR2 | pdb_00006xr2

Computationally designed right-handed alpha/alpha homotrimeric toroid with 3 repeats per subunit

7SQ3 | pdb_00007sq3

Designed trefoil knot protein, variant 1

7SQ4 | pdb_00007sq4

Designed trefoil knot protein, variant 2

7SQ5 | pdb_00007sq5

Designed trefoil knot protein, variant 3

8ETQ | pdb_00008etq

Designed pentafoil knot protein folded into a trefoil knot

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Symmetry Type

SCOP Classification

3UGM | pdb_00003ugm

4YXX | pdb_00004yxx

4YXY | pdb_00004yxy

4YXZ | pdb_00004yxz

4YY2 | pdb_00004yy2

4YY5 | pdb_00004yy5

5BYO | pdb_00005byo

6XR1 | pdb_00006xr1

6XR2 | pdb_00006xr2

7SQ3 | pdb_00007sq3

7SQ4 | pdb_00007sq4

7SQ5 | pdb_00007sq5

8ETQ | pdb_00008etq