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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Aymami, J."

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

Homo sapiens (2)

Taxonomy

Eukaryota (2)

Experimental Method

X-RAY DIFFRACTION (15)

Polymer Entity Type

	DNA (13)
	Protein (3)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (4)
	2.0 - 2.5 (7)
	2.5 - 3.0 (2)

Release Date

	1985 - 1989 (1)
	1990 - 1994 (3)
	1995 - 1999 (3)
	2000 - 2004 (2)
	2005 - 2009 (2)
	2010 - 2014 (1)
	2015 - 2019 (3)

Enzyme Classification Name

Hydrolases (2)

Symmetry Type

	Asymmetric (2)
	Cyclic (1)

SCOP Classification

	All alpha proteins (2)
	Artifacts (1)

AllSelected

1 to 15 of 15 Structures

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121D \| pdb_0000121d	Download File View File

MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

Tabernero, L., Verdaguer, N., Coll, M., Fita, I., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Aymami, J.

(1993) Biochemistry 32: 8403-8410

Released	1994-01-15
Method	X-RAY DIFFRACTION 2.2 Å
Macromolecule	DNA (5'-D(CPGPCPAPAPAPTPTPTPGPCPG)-3') (nucleic acid)
Unique Ligands	NT

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1DNE \| pdb_00001dne	Download File View File

MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2

Coll, M., Aymami, J., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J.

(1989) Biochemistry 28: 310-320

Released	1989-01-09
Method	X-RAY DIFFRACTION 2.4 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPTPAPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	NT

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1DNF \| pdb_00001dnf	Download File View File

EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)

Coll, M., Saal, D., Frederick, C.A., Aymami, J., Rich, A., Wang, A.H.-J.

(1989) Nucleic Acids Res 17: 911-923

Released	1990-10-15
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	DNA (5'-D(CPGPCPGP(UFP)PG)-3') (nucleic acid)
Unique Ligands	MG

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1G3X \| pdb_00001g3x	Download File View File

INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER

Malinina, L., Soler-Lopez, M., Aymami, J., Subirana, J.A.

(2002) Biochemistry 41: 9341-9348

Released	2002-08-16
Method	X-RAY DIFFRACTION 2.7 Å
Macromolecule	N(ALPHA)-(9-ACRIDINOYL)-TETRAARGININE-AMIDE (protein) 5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3' (nucleic acid)
Unique Ligands	MG

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1K9G \| pdb_00001k9g	Download File View File

Crystal Structure of the Complex of Cryptolepine-d(CCTAGG)2

Lisgarten, J.N., Coll, M., Portugal, J., Wright, C.W., Aymami, J.

(2002) Nat Struct Biol 9: 57-60

Released	2001-11-30
Method	X-RAY DIFFRACTION 1.4 Å
Macromolecule	5'-D(CPCPTPAPGPG)-3' (nucleic acid)
Unique Ligands	DR1

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1VTJ \| pdb_00001vtj	Download File View File

MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 1

Coll, M., Aymami, J., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J.

(1989) Biochemistry 28: 310-320

Released	2011-07-13
Method	X-RAY DIFFRACTION 2.4 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPTPAPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	NT

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1Z3F \| pdb_00001z3f	Download File View File

Structure of ellipticine in complex with a 6-bp DNA

Canals, A., Purciolas, M., Aymami, J., Coll, M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1009-1012

Released	2005-07-19
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	5'-D(CPGPAPTPCPG)-3' (nucleic acid)
Unique Ligands	CO, EL

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264D \| pdb_0000264d	Download File View File

THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR-GROOVE-BINDING DRUG HOECHST 33258

Vega, M.C., Garcia-Saez, I., Aymami, J., Eritja, R., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Coll, M.

(1994) Eur J Biochem 222: 721-726

Released	1995-03-31
Method	X-RAY DIFFRACTION 2.44 Å
Macromolecule	DNA (5'-D(CPGPCPAPAPAPTPTPTPGPCPG)-3') (nucleic acid)
Unique Ligands	HT

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2D47 \| pdb_00002d47	Download File View File

MOLECULAR STRUCTURE OF A COMPLETE TURN OF A-DNA

Verdaguer, N., Aymami, J., Fernandez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J., Subirana, J.A.

(1991) J Mol Biology 221: 623-635

Released	1991-10-02
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	DNA (5'-D(CPCPCPCPCPGPCPGPGPGPGPG)-3') (nucleic acid)
Unique Ligands	SPM

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2ET0 \| pdb_00002et0	Download File View File

The structure of a three-way DNA junction in complex with a metallo-supramolecular helicate reveals a new target for drugs

Oleksi, A., Blanco, A.G., Boer, R., Uson, I., Aymami, J., Coll, M.

(2006) Angew Chem Int Ed Engl 45: 1227-1231

Released	2006-03-14
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	5'-D(CPGPTPAPCPG)-3' (nucleic acid)
Unique Ligands	FE2, NPM

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458D \| pdb_0000458d	Download File View File

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG BY A NON-SELF-COMPLEMENTARY AT-RICH SEQUENCE

Aymami, J., Nunn, C.M., Neidle, S.

(1999) Nucleic Acids Res 27: 2691-2698

Released	1999-06-28
Method	X-RAY DIFFRACTION 2.3 Å
Macromolecule	DNA (5'-D(CPGP(CBR)PAPTPAPTPTPTPGPCPG)-3') (nucleic acid) DNA (5'-D(CPGPCPAPAPAPTPAPTPGPCPG)-3') (nucleic acid)

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459D \| pdb_0000459d	Download File View File

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG

Aymami, J., Nunn, C.M., Neidle, S.

(1999) Nucleic Acids Res 27: 2691-2698

Released	1999-06-28
Method	X-RAY DIFFRACTION 2.3 Å
Macromolecule	DNA (5'-D(CPGP(CBR)PAPTPAPTPTPTPGPCPG)-3') (nucleic acid) DNA (5'-D(CPGPCPAPAPAPTPAPTPGPCPG)-3') (nucleic acid)
Unique Ligands	TBZ

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4MNB \| pdb_00004mnb	Download File View File

Crystal Structure of a complex between the marine anticancer drug Variolin B and DNA

Canals, A., Arribas-Bosacoma, R., Alvarez, M., Albericio, F., Aymami, J., Coll, M.

(2017) Sci Rep 7: 39680-39680

Released	2015-03-11
Method	X-RAY DIFFRACTION 1.4 Å
Macromolecule	5'-D(CPGPTPAPCPG)-3' (nucleic acid)
Unique Ligands	CO, NA, NCO, VAR

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5K1I \| pdb_00005k1i	Download File View File

PDE4 crystal structure in complex with small molecule inhibitor

Segarra, V., Hernandez, B., Ferrer-Miralles, N., Korndoerfer, I., Aymami, J.

(2016) J Med Chem 59: 10479-10497

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	6PT, MG, ZN

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5K32 \| pdb_00005k32	Download File View File

PDE4D crystal structure in complex with small molecule inhibitor

Segarra, V., Hernandez, B., Roberts, R., Gracia, J., Soler, M., Bonin, I., Aymami, J.

(2018) J Med Chem 61: 2472-2489

Released	2017-03-29
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	6Q2, EDO, MG, ZN

1 to 15 of 15 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.

121D | pdb_0000121d

MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

1DNE | pdb_00001dne

MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2

1DNF | pdb_00001dnf

EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)

1G3X | pdb_00001g3x

INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER

1K9G | pdb_00001k9g

Crystal Structure of the Complex of Cryptolepine-d(CCTAGG)2

1VTJ | pdb_00001vtj

MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 1

1Z3F | pdb_00001z3f

Structure of ellipticine in complex with a 6-bp DNA

264D | pdb_0000264d

THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR-GROOVE-BINDING DRUG HOECHST 33258

2D47 | pdb_00002d47

MOLECULAR STRUCTURE OF A COMPLETE TURN OF A-DNA

2ET0 | pdb_00002et0

The structure of a three-way DNA junction in complex with a metallo-supramolecular helicate reveals a new target for drugs

458D | pdb_0000458d

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG BY A NON-SELF-COMPLEMENTARY AT-RICH SEQUENCE

459D | pdb_0000459d

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG

4MNB | pdb_00004mnb

Crystal Structure of a complex between the marine anticancer drug Variolin B and DNA

5K1I | pdb_00005k1i

PDE4 crystal structure in complex with small molecule inhibitor

5K32 | pdb_00005k32

PDE4D crystal structure in complex with small molecule inhibitor

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

121D | pdb_0000121d

1DNE | pdb_00001dne

1DNF | pdb_00001dnf

1G3X | pdb_00001g3x

1K9G | pdb_00001k9g

1VTJ | pdb_00001vtj

1Z3F | pdb_00001z3f

264D | pdb_0000264d

2D47 | pdb_00002d47

2ET0 | pdb_00002et0

458D | pdb_0000458d

459D | pdb_0000459d

4MNB | pdb_00004mnb

5K1I | pdb_00005k1i

5K32 | pdb_00005k32