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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Bolduc, J."

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Search Summary

This query matches 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

synthetic construct (9)

Taxonomy

other sequences (9)

Experimental Method

X-RAY DIFFRACTION (9)

Polymer Entity Type

Protein (9)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (5)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (3)
	2015 - 2019 (6)

Symmetry Type

	Asymmetric (8)
	Cyclic (1)

SCOP Classification

	Alpha and beta proteins (a/b) (3)
	Artifacts (3)

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1 to 9 of 9 Structures

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3NXF \| pdb_00003nxf	Download File View File

Robust computational design, optimization, and structural characterization of retroaldol enzymes

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.

(2012) J Mol Biology 415: 615-625

Released	2011-06-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	synthetic construct
Macromolecule	Retro-Aldolase (protein)
Unique Ligands	SO4

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3O6Y \| pdb_00003o6y	Download File View File

Robust computational design, optimization, and structural characterization of retroaldol enzymes

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.

(2012) J Mol Biology 415: 615-625

Released	2011-06-29
Method	X-RAY DIFFRACTION 2.091 Å
Organisms	synthetic construct
Macromolecule	Retro-Aldolase (protein)
Unique Ligands	SO4

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3UD6 \| pdb_00003ud6	Download File View File

Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design

Baker, D., Stoddard, B.L., Althoff, E.A., Wang, L., Jiang, L., Moody, J., Bolduc, J., Lassila, J., Hilvert, D.

(2012) J Mol Biology 415: 615-625

Released	2011-11-23
Method	X-RAY DIFFRACTION 2.091 Å
Organisms	synthetic construct
Macromolecule	RETRO-ALDOLASE (protein)
Unique Ligands	3NK, SO4

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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)

1 to 9 of 9 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.

3NXF | pdb_00003nxf

Robust computational design, optimization, and structural characterization of retroaldol enzymes

3O6Y | pdb_00003o6y

Robust computational design, optimization, and structural characterization of retroaldol enzymes

3UD6 | pdb_00003ud6

Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design

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

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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

3NXF | pdb_00003nxf

3O6Y | pdb_00003o6y

3UD6 | pdb_00003ud6

4YXX | pdb_00004yxx

4YXY | pdb_00004yxy

4YXZ | pdb_00004yxz

4YY2 | pdb_00004yy2

4YY5 | pdb_00004yy5

5BYO | pdb_00005byo