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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "van der Marel, G.A."

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Search Summary

This query matches 165 Structures.

Refinements

Structure Determination Methodology

experimental (165)

Scientific Name of Source Organism

	Saccharomyces cerevisiae S288C (44)
	Homo sapiens (39)
	Cellvibrio japonicus Ueda107 (8)
	Aspergillus oryzae (5)
	Escherichia coli (4)
	Niallia circulans (4)
	synthetic construct (4)
	Bacteroides thetaiotaomicron VPI-5482 (3)
	Cellvibrio japonicus (3)
	Saccharomyces cerevisiae (3)

More...

Taxonomy

	Eukaryota (85)
	Bacteria (39)
	other sequences (4)

Experimental Method

	X-RAY DIFFRACTION (158)
	SOLUTION NMR (7)

Polymer Entity Type

	Protein (123)
	DNA (45)
	NA-hybrid (2)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (24)
	1.5 - 2.0 (52)
	2.0 - 2.5 (28)
	2.5 - 3.0 (38)
	3.0 - 3.5 (14)

Release Date

	1985 - 1989 (3)
	1990 - 1994 (23)
	1995 - 1999 (8)
	2000 - 2004 (6)
	2005 - 2009 (1)
	2010 - 2014 (17)
	2015 - 2019 (70)
	2020 - 2024 (37)

Enzyme Classification Name

	Hydrolases (95)
	Transferases (13)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (62)
	Cyclic (62)

SCOP Classification

	Alpha and beta proteins (a+b) (46)
	Artifacts (48)
	All beta proteins (9)
	Alpha and beta proteins (a/b) (9)
	All alpha proteins (4)

AllSelected

1 to 25 of 165 Structures

Page 1 of 7

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Explore in 3D

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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127D \| pdb_0000127d	Download File View File

DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3') COMPLEXED WITH HOECHST 33258

Sriram, M., Van Der Marel, G.A., Roelen, H.L.P.F., Van Boom, J.H., Wang, A.H.-J.

(1992) EMBO J 11: 225-232

Released	1994-01-15
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	HT

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128D \| pdb_0000128d	Download File View File

MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST 33258

Sriram, M., Van Der Marel, G.A., Roelen, H.L.P.F., Van Boom, J.H., Wang, A.H.-J.

(1992) EMBO J 11: 225-232

Released	1994-01-15
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	DNA (5'-D(CPGPCP(G36)PAPAPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	HT

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129D \| pdb_0000129d	Download File View File

DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3') COMPLEXED WITH HOECHST 33342

Sriram, M., Van Der Marel, G.A., Roelen, H.L.P.F., Van Boom, J.H., Wang, A.H.-J.

(1992) EMBO J 11: 225-232

Released	1994-01-15
Method	X-RAY DIFFRACTION 2.25 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	HT1

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130D \| pdb_0000130d	Download File View File

MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST 33342

Sriram, M., Van Der Marel, G.A., Roelen, H.L.P.F., Van Boom, J.H., Wang, A.H.-J.

(1992) EMBO J 11: 225-232

Released	1994-01-15
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	DNA (5'-D(CPGPCP(G36)PAPAPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	HT1

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1AC7 \| pdb_00001ac7	Download File View File

STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTAGTTATAGGAT): THE FORMATION OF A G-A BASE PAIR IN THE LOOP, NMR, 10 STRUCTURES

Van Dongen, M.J.P., Mooren, M.M.W., Willems, E.F.A., Van Der Marel, G.A., Van Boom, J.H., Wijmenga, S.S., Hilbers, C.W.

(1997) Nucleic Acids Res 25: 1537-1547

Released	1997-07-07
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(APTPCPCPTPAPGPTPTPAPTPAPGPGPAPT)-3') (nucleic acid)

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1B4Y \| pdb_00001b4y	Download File View File

STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN INTRAMOLECULAR DNA TRIPLE HELIX.

Van Dongen, M.J.P., Doreleijers, J.F., Van Der Marel, G.A., Van Boom, J.H., Hilbers, C.W., Wijmenga, S.S.

(1999) Nat Struct Biol 6: 854-859

Released	1999-09-13
Method	SOLUTION NMR
Macromolecule	DNA (H-Y5 TRIPLE HELIX) (nucleic acid)

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1CJG \| pdb_00001cjg	Download File View File

NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX

Spronk, C.A.E.M., Bonvin, A.M.J.J., Radha, P.K., Melacini, G., Boelens, R., Kaptein, R.

(1999) Structure 7: 1483-1492

Released	2000-01-01
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PROTEIN (LAC REPRESSOR) (protein) DNA (5'-D(GPAPAPTPTPGPTPGPAPGPCPGPCPTPCPAPCPAPAPTPTPC)-3') (nucleic acid)

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1D10 \| pdb_00001d10	Download File View File

STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCIN AND DAUNOMYCIN

Frederick, C.A., Williams, L.D., Ughetto, G., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J.

(1990) Biochemistry 29: 2538-2549

Released	1990-10-15
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	DNA (5'-D(CPGPAPTPCPG)-3') (nucleic acid)
Unique Ligands	DM1, NA, SPM

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1D12 \| pdb_00001d12	Download File View File

STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCIN AND DAUNOMYCIN

Frederick, C.A., Williams, L.D., Ughetto, G., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J.

(1990) Biochemistry 29: 2538-2549

Released	1990-10-15
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	DNA (5'-D(CPGPAPTPCPG)-3') (nucleic acid)
Unique Ligands	DM2, NA, SPM

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1D13 \| pdb_00001d13	Download File View File

MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)

Frederick, C.A., Quigley, G.J., Teng, M.-K., Coll, M., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J.

(1989) Eur J Biochem 181: 295-307

Released	1990-10-15
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	DNA (5'-D(APCPCPGPGPCPCPGPGPT)-3') (nucleic acid)

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1D14 \| pdb_00001d14	Download File View File

STRUCTURE OF 11-DEOXYDAUNOMYCIN BOUND TO DNA CONTAINING A PHOSPHOROTHIOATE

Williams, L.D., Egli, M., Ughetto, G., Van Der Marel, G.A., Van Boom, J.H., Quigley, G.J., Wang, A.H.-J., Rich, A., Frederick, C.A.

(1990) J Mol Biology 215: 313-320

Released	1990-10-15
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	DNA (5'-D(CPGPTP(AS)PCPG)-3') (nucleic acid)
Unique Ligands	DM3

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1D17 \| pdb_00001d17	Download File View File

DNA-NOGALAMYCIN INTERACTIONS

Egli, M., Williams, L.D., Frederick, C.A., Rich, A.

(1991) Biochemistry 30: 1364-1372

Released	1991-07-15
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	DNA (5'-D((5CM)PGPTPAP(5CM)PG)-3') (nucleic acid)
Unique Ligands	NGM

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1D21 \| pdb_00001d21	Download File View File

BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON

Gao, Y.-G., Liaw, Y.-C., Robinson, H., Wang, A.H.-J.

(1990) Biochemistry 29: 10307-10316

Released	1991-07-15
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	DNA (5'-D((5CM)PGPTP(AS)P(5CM)PG)-3') (nucleic acid)
Unique Ligands	NGM

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1D22 \| pdb_00001d22	Download File View File

BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON

Gao, Y.-G., Liaw, Y.-C., Robinson, H., Wang, A.H.-J.

(1990) Biochemistry 29: 10307-10316

Released	1991-07-15
Method	X-RAY DIFFRACTION 1.8 Å
Macromolecule	DNA (5'-D((5CM)PGPTP(AS)P(5CM)PG)-3') (nucleic acid)
Unique Ligands	NGU

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1D35 \| pdb_00001d35	Download File View File

FACILE FORMATION OF A CROSSLINKED ADDUCT BETWEEN DNA AND THE DAUNORUBICIN DERIVATIVE MAR70 MEDIATED BY FORMALDEHYDE: MOLECULAR STRUCTURE OF THE MAR70-D(CGTNACG) COVALENT ADDUC

Gao, Y.-G., Liaw, Y.-C., Li, Y.-K., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.

(1991) Proc Natl Acad Sci U S A 88: 4845-4849

Released	1992-04-15
Method	X-RAY DIFFRACTION 1.3 Å
Macromolecule	DNA (5'-D(CPGPTP(A40)PCPG)-3') (nucleic acid)
Unique Ligands	MAR, MG

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1D36 \| pdb_00001d36	Download File View File

FACILE FORMATION OF A CROSSLINKED ADDUCT BETWEEN DNA AND THE DAUNORUBICIN DERIVATIVE MAR70 MEDIATED BY FORMALDEHYDE: MOLECULAR STRUCTURE OF THE MAR70-D(CGTNACG) COVALENT ADDUC

Gao, Y.-G., Liaw, Y.-C., Li, Y.-K., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.

(1991) Proc Natl Acad Sci U S A 88: 4845-4849

Released	1992-04-15
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	DNA (5'-D(CPGPTPAPCPG)-3') (nucleic acid)
Unique Ligands	MAR, MG

Explore in 3D

1D37 \| pdb_00001d37	Download File View File

INFLUENCE OF AGLYCONE MODIFICATIONS ON THE BINDING OF ANTHRACYCLINE DRUGS TO DNA: THE MOLECULAR STRUCTURE OF IDARUBICIN AND 4-O-DEMETHYL-11-DEOXYDOXORUBICIN COMPLEXED TO D(CGATCG)

Gao, Y.-G., Wang, A.H.-J.

(1991) Anticancer Drug Des 6: 137-149

Released	1992-04-15
Method	X-RAY DIFFRACTION 1.8 Å
Macromolecule	DNA (5'-D(CPGPAPTPCPG)-3') (nucleic acid)
Unique Ligands	DM4

Explore in 3D

1D38 \| pdb_00001d38	Download File View File

INFLUENCE OF AGLYCONE MODIFICATIONS ON THE BINDING OF ANTHRACYCLINE DRUGS TO DNA: THE MOLECULAR STRUCTURE OF IDARUBICIN AND 4-O-DEMETHYL-11-DEOXYDOXORUBICIN COMPLEXED TO D(CGATCG)

Gao, Y.-G., Wang, A.H.-J.

(1991) Anticancer Drug Des 6: 137-149

Released	1992-04-15
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	DNA (5'-D(CPGPAPTPCPG)-3') (nucleic acid)
Unique Ligands	DM5, MG

Explore in 3D

1D85 \| pdb_00001d85	Download File View File

STRUCTURAL CONSEQUENCES OF A CARCINOGENIC ALKYLATION LESION ON DNA: EFFECT OF O6-ETHYL-GUANINE ON THE MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG)-NETROPSIN COMPLEX

Sriram, M., Van Der Marel, G.A., Roelen, H.L.P.F., Van Boom, J.H., Wang, A.H.-J.

(1992) Biochemistry 31: 11823-11834

Released	1993-07-15
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	DNA (5'-D(CPGPCP(G36)PAPAPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	NT

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1D86 \| pdb_00001d86	Download File View File

STRUCTURAL CONSEQUENCES OF A CARCINOGENIC ALKYLATION LESION ON DNA: EFFECT OF O6-ETHYL-GUANINE ON THE MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG)-NETROPSIN COMPLEX

Sriram, M., Van Der Marel, G.A., Roelen, H.L.P.F., Van Boom, J.H., Wang, A.H.-J.

(1992) Biochemistry 31: 11823-11834

Released	1993-07-15
Method	X-RAY DIFFRACTION 2.2 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	NT

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1D96 \| pdb_00001d96	Download File View File

MOLECULAR STRUCTURE OF R(GCG)D(TATACGC): A DNA-RNA HYBRID HELIX JOINED TO DOUBLE HELICAL DNA

Wang, A.H.-J., Fujii, S., Van Boom, J.H., Van Der Marel, G.A., Van Boeckel, S.A.A., Rich, A.

(1982) Nature 299: 601-604

Released	1993-07-15
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	DNA/RNA (5'-R(GPCPGP)-D(TPAPTPAPCPGP*C)-3') (hybrid)

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1DCG \| pdb_00001dcg	Download File View File

THE MOLECULAR STRUCTURE OF THE LEFT-HANDED Z-DNA DOUBLE HELIX AT 1.0 ANGSTROM ATOMIC RESOLUTION. GEOMETRY, CONFORMATION, AND IONIC INTERACTIONS OF D(CGCGCG)

Gessner, R.V., Frederick, C.A., Quigley, G.J., Rich, A., Wang, A.H.-J.

(1989) J Biological Chem 264: 7921-7935

Released	1989-01-09
Method	X-RAY DIFFRACTION 1 Å
Macromolecule	DNA (5'-D(CPGPCPGPCPG)-3') (nucleic acid)
Unique Ligands	MG

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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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1LCC \| pdb_00001lcc	Download File View File

STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS

Chuprina, V.P., Rullmann, J.A.C., Lamerichs, R.M.J.N., Van Boom, J.H., Boelens, R., Kaptein, R.

(1993) J Mol Biology 234: 446-462

Released	1994-01-31
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	Lac Repressor (protein) DNA (5'-D(APAPTPTPGPTPGPAPGPCPG)-3') (nucleic acid) DNA (5'-D(CPGPCPTPCPAPCPAPAPTPT)-3') (nucleic acid)
Unique Ligands	NA

1 to 25 of 165 Structures

Page 1 of 7

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

121D | pdb_0000121d

127D | pdb_0000127d

128D | pdb_0000128d

129D | pdb_0000129d

130D | pdb_0000130d

1AC7 | pdb_00001ac7

1B4Y | pdb_00001b4y

1CJG | pdb_00001cjg

1D10 | pdb_00001d10

1D12 | pdb_00001d12

1D13 | pdb_00001d13

1D14 | pdb_00001d14

1D17 | pdb_00001d17

1D21 | pdb_00001d21

1D22 | pdb_00001d22

1D35 | pdb_00001d35

1D36 | pdb_00001d36

1D37 | pdb_00001d37

1D38 | pdb_00001d38

1D85 | pdb_00001d85

1D86 | pdb_00001d86

1D96 | pdb_00001d96

1DCG | pdb_00001dcg

1DNE | pdb_00001dne

1LCC | pdb_00001lcc