RCSB PDB: Search

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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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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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

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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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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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1IEK \| pdb_00001iek	Download File View File

SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY (DIAESTEREOISOMER S)

Soliva, R., Monaco, V., Gomez-Pinto, I., Meeuwenoord, N.J., van der Marel, G.A., van Boom, J.H., Gonzalez, C., Orozco, M.

(2001) Nucleic Acids Res 29: 2973-2985

Released	2001-07-25
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPAPCPCP(OCT)GPGPAPAPC)-3' (nucleic acid) 5'-D(GPTPTPCPCPGPGPTPGPG)-3' (nucleic acid)
Unique Ligands	OCT

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1IEY \| pdb_00001iey	Download File View File

SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY (DIAESTEREOISOMER R)

Soliva, R., Monaco, V., Gomez-Pinto, I., Meeuwenoord, N.J., van der Marel, G.A., van Boom, J.H., Gonzalez, C., Orozco, M.

(2001) Nucleic Acids Res 29: 2973-2985

Released	2001-07-25
Method	SOLUTION NMR
Macromolecule	5'-D(GPTPTPCPCPGPGPTPGPG)-3' (nucleic acid) 5'-D(PCPCPAPCPCP(OCT)GPGPAPAPC)-3' (nucleic acid)
Unique Ligands	OCT

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1NDN \| pdb_00001ndn	Download File View File

MOLECULAR STRUCTURE OF NICKED DNA. MODEL T4

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

(1990) Proc Natl Acad Sci U S A 87: 2526-2530

Released	1992-07-14
Method	X-RAY DIFFRACTION 3 Å
Macromolecule	DNA (5'-D(CPGPCPGPAPAPAPAPCPGPCPG)-3') (nucleic acid) DNA (5'-D(CPGPCPGPTPT)-3') (nucleic acid) DNA (5'-D(TPTPCPGPCPG)-3') (nucleic acid)

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1O55 \| pdb_00001o55	Download File View File

MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION

Gao, Y.G., Robinson, H., Guan, Y., Liaw, Y.C., van Boom, J.H., van der Marel, G.A., Wang, A.H.

(1998) J Biomol Struct Dyn 16: 69-76

Released	2003-08-26
Method	X-RAY DIFFRACTION 1.04 Å
Macromolecule	DNA (5'-CD(APAP*AP)-3') (nucleic acid)
Unique Ligands	CO

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1O56 \| pdb_00001o56	Download File View File

MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION

Gao, Y.G., Robinson, H., Guan, Y., Liaw, Y.C., van Boom, J.H., van der Marel, G.A., Wang, A.H.

(1998) J Biomol Struct Dyn 16: 69-76

Released	2003-08-26
Method	X-RAY DIFFRACTION 0.9 Å
Macromolecule	DNA (5'-CD(APAPAP)-3') (nucleic acid)

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1UZ6 \| pdb_00001uz6	Download File View File

anti-Lewis X Fab fragment uncomplexed

Van Roon, A.M.M., Pannu, N.S., De Vrind, J.P.M., Hokke, C.H., Deelder, A.M., Van Der marel, G.A., Van Boom, J.H., Abrahams, J.P.

(2004) Structure 12: 1227

Released	2004-06-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Mus musculus
Macromolecule	IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A (protein) IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A (protein)
Unique Ligands	SO4

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1UZ8 \| pdb_00001uz8	Download File View File

anti-Lewis X Fab fragment in complex with Lewis X

Van Roon, A.M.M., Pannu, N.S., De Vrind, J.P.M., Hokke, C.H., Deelder, A.M., Van Der marel, G.A., Van Boom, J.H., Abrahams, J.P.

(2004) Structure 12: 1227

Released	2004-06-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus
Macromolecule	IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A (protein) IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A (protein)
Unique branched monosaccharides	FUC, GAL, MAG

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1VTE \| pdb_00001vte	Download File View File

MOLECULAR STRUCTURE OF NICKED DNA. MODEL A4

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

(1990) Proc Natl Acad Sci U S A 87: 2526-2530

Released	2011-07-13
Method	X-RAY DIFFRACTION 3 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(CPGPCPGPAPAPAPAPCPGPCPG)-3') (nucleic acid) DNA (5'-D(CPGPCPGPTPT)-3') (nucleic acid) DNA (5'-D(TPTPCPGPCPG)-3') (nucleic acid)

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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

127D | pdb_0000127d

128D | pdb_0000128d

129D | pdb_0000129d

130D | pdb_0000130d

1AC7 | pdb_00001ac7

1B4Y | pdb_00001b4y

1D10 | pdb_00001d10

1D12 | pdb_00001d12

1D13 | pdb_00001d13

1D14 | pdb_00001d14

1D35 | pdb_00001d35

1D36 | pdb_00001d36

1D85 | pdb_00001d85

1D86 | pdb_00001d86

1D96 | pdb_00001d96

1DNE | pdb_00001dne

1IEK | pdb_00001iek

1IEY | pdb_00001iey

1NDN | pdb_00001ndn

1O55 | pdb_00001o55

1O56 | pdb_00001o56

1UZ6 | pdb_00001uz6

1UZ8 | pdb_00001uz8

1VTE | pdb_00001vte