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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "DeGrado, W.F."

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Search Summary

This query matches 77 Structures.

Refinements

Structure Determination Methodology

experimental (77)

Scientific Name of Source Organism

	synthetic construct (41)
	Homo sapiens (7)
	Escherichia coli (4)
	Influenza A virus (4)
	Influenza A virus (A/Hickox/1940(H1N1)) (3)
	Influenza A virus (A/udorn/1972(H3N2)) (3)
	Influenza A virus (A/Jinfang/132/2002(H3N2)) (2)
	Rattus norvegicus (2)
	H3N2 subtype (1)
	Helicana (1)

More...

Taxonomy

	other sequences (41)
	Riboviria (17)
	Eukaryota (8)
	Bacteria (4)
	Riboviria (RNA viruses and viroids) (1)

Experimental Method

	X-RAY DIFFRACTION (63)
	SOLUTION NMR (12)
	SOLID-STATE NMR (2)

Polymer Entity Type

Protein (77)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (13)
	1.5 - 2.0 (21)
	2.0 - 2.5 (11)
	2.5 - 3.0 (12)
	3.0 - 3.5 (3)
	3.5 - 4.0 (2)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (4)
	2000 - 2004 (2)
	2005 - 2009 (5)
	2010 - 2014 (12)
	2015 - 2019 (32)
	2020 - 2024 (20)
	2025 - 2029 (1)

Membrane Protein Annotation

	PDBTM (18)
	MemProtMD (15)
	OPM (13)
	mpstruc (11)

Symmetry Type

	Cyclic (46)
	Asymmetric (23)
	Dihedral (12)

SCOP Classification

	All beta proteins (5)
	Designed proteins (10)

AllSelected

1 to 25 of 77 Structures

Page 1 of 4

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1AL1 \| pdb_00001al1	Download File View File

CRYSTAL STRUCTURE OF ALPHA1: IMPLICATIONS FOR PROTEIN DESIGN

Hill, C.P., Anderson, D.H., Wesson, L., Degrado, W.F., Eisenberg, D.

(1990) Science 249: 543-546

Released	1991-10-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	synthetic construct
Macromolecule	ALPHA HELIX PEPTIDE: ELLKKLLEELKG (protein)
Unique Ligands	SO4

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1COI \| pdb_00001coi	Download File View File

DESIGNED TRIMERIC COILED COIL-VALD

Ogihara, N.L., Weiss, M.S., Degrado, W.F., Eisenberg, D.

(1997) Protein Sci 6: 80-88

Released	1997-02-12
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	synthetic construct
Macromolecule	COIL-VALD (protein)
Unique Ligands	SO4

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1G6U \| pdb_00001g6u	Download File View File

CRYSTAL STRUCTURE OF A DOMAIN SWAPPED DIMER

Ogihara, N.L., Ghirlanda, G., Bryson, J.W., Gingery, M., DeGrado, W.F., Eisenberg, D.

(2001) Proc Natl Acad Sci U S A 98: 1404-1409

Released	2001-02-21
Method	X-RAY DIFFRACTION 1.48 Å
Macromolecule	DOMAIN SWAPPED DIMER (protein)
Unique Ligands	SO4, TFA

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1NVO \| pdb_00001nvo	Download File View File

Solution structure of a four-helix bundle model, apo-DF1

Maglio, O., Nastri, F., Pavone, V., Lombardi, A., DeGrado, W.F.

(2003) Proc Natl Acad Sci U S A 100: 3772-3777

Released	2003-03-25
Method	SOLUTION NMR
Macromolecule	Homodimeric Alpha2 Four-Helix Bundle (protein)

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1QP6 \| pdb_00001qp6	Download File View File

SOLUTION STRUCTURE OF ALPHA2D

Hill, R.B., DeGrado, W.F.

(1998) J Am Chem Soc 120: 1138-1145

Released	1999-06-09
Method	SOLUTION NMR
Macromolecule	PROTEIN (ALPHA2D) (protein)

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1U7J \| pdb_00001u7j	Download File View File

Solution structure of a diiron protein model

Maglio, O., Nastri, F., Calhoun, J.R., Lahr, S., Pavone, V., DeGrado, W.F., Lombardi, A.

(2005) J Mol Biology 346: 1441-1454

Released	2005-03-01
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	Four-helix bundle model (protein)
Unique Ligands	ZN

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1U7M \| pdb_00001u7m	Download File View File

Solution structure of a diiron protein model: Due Ferri(II) turn mutant

Maglio, O., Nastri, F., Calhoun, J.R., Lahr, S., Pavone, V., DeGrado, W.F., Lombardi, A.

(2005) J Mol Biology 346: 1441-1454

Released	2005-03-01
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	Four-helix bundle model (protein)
Unique Ligands	ZN

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1Y47 \| pdb_00001y47	Download File View File

Structural studies of designed alpha-helical hairpins

Lahr, S.J., Engel, D.E., Stayrook, S.E., Maglio, O., North, B., Geremia, S., Lombardi, A., DeGrado, W.F.

(2005) J Mol Biology 346: 1441-1454

Released	2005-03-22
Method	X-RAY DIFFRACTION 2.7 Å
Macromolecule	dueferri (DF2) (protein)
Unique Ligands	CD

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1YOD \| pdb_00001yod	Download File View File

Crystal structure of a water soluble analog of phospholamban

Slovic, A.M., Stayrook, S.E., North, B., DeGrado, W.F.

(2005) J Mol Biology 348: 777-787

Released	2005-04-19
Method	X-RAY DIFFRACTION 1.8 Å
Macromolecule	water-solublized phospholamban (protein)

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2A3D \| pdb_00002a3d	Download File View File

SOLUTION STRUCTURE OF A DE NOVO DESIGNED SINGLE CHAIN THREE-HELIX BUNDLE (A3D)

Walsh, S.T.R., Cheng, H., Bryson, J.W., Roder, H., Degrado, W.F.

(1999) Proc Natl Acad Sci U S A 96: 5486-5491

Released	1999-05-05
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	PROTEIN (DE NOVO THREE-HELIX BUNDLE) (protein)

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2HZ8 \| pdb_00002hz8	Download File View File

QM/MM structure refined from NMR-structure of a single chain diiron protein

Calhoun, J.R., Liu, W., Spiegel, K., Dal Peraro, M., Klein, M.L., Wand, A.J., DeGrado, W.F.

(2008) Structure 16: 210-215

Released	2007-07-17
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	De novo designed diiron protein (protein)
Unique Ligands	ZN

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2KQT \| pdb_00002kqt	Download File View File

Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine

Cady, S.D., Schmidt-Rohr, K., Wang, J., Soto, C.S., DeGrado, W.F., Hong, M.

(2010) Nature 463: 689-692

Released	2010-02-09
Method	SOLID-STATE NMR
Organisms	Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd)
Macromolecule	M2 protein (protein)
Unique Ligands	308

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2MUZ \| pdb_00002muz	Download File View File

ssNMR structure of a designed rocker protein

Wang, T., Joh, N., Wu, Y., DeGrado, W.F., Hong, M.

(2014) Science 346: 1520-1524

Released	2014-12-24
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	designed rocker protein (protein)

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3AL1 \| pdb_00003al1	Download File View File

DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM

Patterson, W.R., Anderson, D.H., Degrado, W.F., Cascio, D., Eisenberg, D.

(1999) Protein Sci 8: 1410-1422

Released	1998-11-04
Method	X-RAY DIFFRACTION 0.75 Å
Macromolecule	PROTEIN (D, L-ALPHA-1) (protein)
Unique Ligands	ETA, MPD

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3LBW \| pdb_00003lbw	Download File View File

High resolution crystal structure of transmembrane domain of M2

Acharya, R., Polishchuk, A.L., DeGrado, W.F.

(2010) Proc Natl Acad Sci U S A 107: 15075-15080

Released	2010-07-28
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	H3N2 subtype
Macromolecule	M2 protein (protein)
Unique Ligands	PEG, XYL, Z82

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3S0R \| pdb_00003s0r	Download File View File

Crystal Structure of De novo Designed helical assembly protein

Acharya, R., Grigoryan, G., Kim, Y.H., DeGrado, W.F.

(2011) Science 332: 1071-1076

Released	2011-06-15
Method	X-RAY DIFFRACTION 2.453 Å
Organisms	synthetic construct
Macromolecule	De novo designed Helical Assembly (protein)

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4JFX \| pdb_00004jfx	Download File View File

Structure of phosphotyrosine (pTyr) scaffold bound to pTyr peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-09-25
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PG4

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4JFY \| pdb_00004jfy	Download File View File

Apo structure of phosphotyrosine (pYAb) scaffold

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 2.63 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	PG4

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4JFZ \| pdb_00004jfz	Download File View File

Structure of phosphoserine (pSAb) scaffold bound to pSer peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PPI

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4JG0 \| pdb_00004jg0	Download File View File

Structure of phosphoserine/threonine (pSTAb) scaffold bound to pSer peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PPI

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4JG1 \| pdb_00004jg1	Download File View File

Structure of phosphoserine/threonine (pSTAb) scaffold bound to pThr peptide

Koerber, J.T., Thomsen, N.D., Hannigan, B.T., Degrado, W.F., Wells, J.A.

(2013) Nat Biotechnol 31: 916-921

Released	2013-08-28
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) Phosphopeptide (protein)
Unique Ligands	PPI

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4P6J \| pdb_00004p6j	Download File View File

Crystal Structure of the Computationally Designed Transmembrane Metallotransporter with 4-bromophenylalanine in Octyl Glucoside

Joh, N.H., Acharya, R., DeGrado, W.F.

(2014) Science 346: 1520-1524

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	synthetic construct
Macromolecule	Computationally Designed Transporter of Zn(II) and Proton (protein)
Unique Ligands	SO4

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4P6K \| pdb_00004p6k	Download File View File

Crystal Structure of the Computationally Designed Transmembrane Metallotransporter with 4-bromophenylalanine in Lipidic Cubic Phase

Joh, N.H., Acharya, R., DeGrado, W.F.

(2014) Science 346: 1520-1524

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.704 Å
Organisms	synthetic construct
Macromolecule	Computationally Designed Transporter of Zn(II) and Proton (protein)

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4P6L \| pdb_00004p6l	Download File View File

Crystal Structure of the Computationally Designed Transmembrane Metallotransporter in Octyl Glucoside

Joh, N.H., Acharya, R., DeGrado, W.F.

(2014) Science 346: 1520-1524

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.803 Å
Organisms	synthetic construct
Macromolecule	Computationally Designed Transporter of Zn(II) and proton (protein)

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4QKC \| pdb_00004qkc	Download File View File

Influenza A M2 wild type TM domain at low pH in the lipidic cubic phase under cryo diffraction conditions

Thomaston, J.L., DeGrado, W.F.

(2015) Proc Natl Acad Sci U S A 112: 14260-14265

Released	2015-11-11
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Influenza A virus (A/udorn/1972(H3N2))
Macromolecule	influenza M2 monomer (protein)
Unique Ligands	CA, CL, EDO, OLB

1 to 25 of 77 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1AL1 | pdb_00001al1

1COI | pdb_00001coi

1G6U | pdb_00001g6u

1NVO | pdb_00001nvo

1QP6 | pdb_00001qp6

1U7J | pdb_00001u7j

1U7M | pdb_00001u7m

1Y47 | pdb_00001y47

1YOD | pdb_00001yod

2A3D | pdb_00002a3d

2HZ8 | pdb_00002hz8

2KQT | pdb_00002kqt

2MUZ | pdb_00002muz

3AL1 | pdb_00003al1

3LBW | pdb_00003lbw

3S0R | pdb_00003s0r

4JFX | pdb_00004jfx

4JFY | pdb_00004jfy

4JFZ | pdb_00004jfz

4JG0 | pdb_00004jg0

4JG1 | pdb_00004jg1

4P6J | pdb_00004p6j

4P6K | pdb_00004p6k

4P6L | pdb_00004p6l

4QKC | pdb_00004qkc