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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Collins, R.F."

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

	Homo sapiens (14)
	synthetic construct (2)
	Leishmania donovani (1)

Taxonomy

	Eukaryota (15)
	other sequences (2)

Experimental Method

X-RAY DIFFRACTION (15)

Polymer Entity Type

	Protein (15)
	DNA (12)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (11)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (12)
	2005 - 2009 (1)
	2015 - 2019 (2)

Enzyme Classification Name

	Hydrolases (13)
	Isomerases (2)

Symmetry Type

	Asymmetric (15)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a+b) (12)
	All alpha proteins (1)
	Artifacts (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 15 of 15 Structures

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1JY1 \| pdb_00001jy1	Download File View File

CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.J.

(2002) Structure 10: 237-248

Released	2002-02-20
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Homo sapiens
Macromolecule	TYROSYL-DNA PHOSPHODIESTERASE (protein)

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1MU7 \| pdb_00001mu7	Download File View File

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Tungstate Complex

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.J.

(2003) J Mol Biology 324: 917-932

Released	2003-01-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA Phosphodiesterase (protein)
Unique Ligands	GOL, WO4

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1MU9 \| pdb_00001mu9	Download File View File

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.J.

(2002) J Mol Biology 324: 917-932

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA Phosphodiesterase (protein)
Unique Ligands	GOL, VO4

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1NOP \| pdb_00001nop	Download File View File

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.J.

(2003) Chem Biol 10: 139-147

Released	2003-03-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	topoisomerase I-derived peptide (protein) tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPAPGPTPT)-3' (nucleic acid)
Unique Ligands	VO4

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1R49 \| pdb_00001r49	Download File View File

Human topoisomerase I (Topo70) double mutant K532R/Y723F

Interthal, H., Quigley, P.M., Hol, W.G., Champoux, J.J.

(2004) J Biological Chem 279: 2984-2992

Released	2003-12-16
Method	X-RAY DIFFRACTION 3.13 Å
Organisms	Homo sapiens
Macromolecule	DNA topoisomerase I (protein) 5'-D(APAPAPAPAPGPAPCPTPTPAPGPAPAPAPAPAPTPTPTPTPT)-3' (nucleic acid) 5'-D(PAPAPAPAPAPTPTPTPTPTPCPTPAPAPGPTPCPTPTPTPTPT)-3' (nucleic acid)

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1RFF \| pdb_00001rff	Download File View File

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Topoisomerase I-Derived Peptide (protein) Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPTPT)-3' (nucleic acid)
Unique Ligands	SPM, VO4

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1RFI \| pdb_00001rfi	Download File View File

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Topoisomerase I-Derived Peptide (protein) Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPTPC)-3' (nucleic acid)
Unique Ligands	SPM, VO4

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1RG1 \| pdb_00001rg1	Download File View File

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPTPT)-3' (nucleic acid)
Unique Ligands	OTS, SPM, VO4

Explore in 3D

1RG2 \| pdb_00001rg2	Download File View File

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPTPA)-3' (nucleic acid)
Unique Ligands	OTR, OTS, SPM, VO4

Explore in 3D

1RGT \| pdb_00001rgt	Download File View File

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPTPC)-3' (nucleic acid)
Unique Ligands	OTR, OTS, SPM, VO4

Explore in 3D

1RGU \| pdb_00001rgu	Download File View File

The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.22 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(APGPTPG)-3' (nucleic acid)
Unique Ligands	OTS, SPM, VO4

Explore in 3D

1RH0 \| pdb_00001rh0	Download File View File

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT

Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

(2004) J Med Chem 47: 829-837

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) 5'-D(GPTP*T)-3' (nucleic acid)
Unique Ligands	OTS, SPM, VO4

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2B9S \| pdb_00002b9s	Download File View File

Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex

Davies, D.R., Hol, W.G.J.

(2006) J Mol Biology 357: 1202-1210

Released	2006-01-17
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Leishmania donovani
Macromolecule	DNA topoisomerase I-like protein (protein) topoisomerase I-like protein (protein) 5'-D(APAPAPAPAPGPAPCPTPT)-3' (nucleic acid) 5'-D(APAPAPAPAPTPTPTPTPTPCPTPAPAPGPTPCPTPTPTPTPT)-3' (nucleic acid) 5'-D(APGPAPAPAPAPAPTPTPTPTPT)-3' (nucleic acid)
Unique Ligands	VO4

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5NW9 \| pdb_00005nw9	Download File View File

Crystal structure of the complex of Tdp1 with duplex DNA

Richardson, J.M., Ruksenaite, E., Morris, E.R.

(2018) Nat Commun 9: 24-24

Released	2018-01-10
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) DNA (5'-D(PTPGPCPGPCPAPGPTP*A)-3') (nucleic acid)

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5NWA \| pdb_00005nwa	Download File View File

Crystal structure of the complex of Tdp1 with duplex DNA

Richardson, J.M., Ruksenaite, E., Morris, E.R.

(2018) Nat Commun 9: 24-24

Released	2018-01-10
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Tyrosyl-DNA phosphodiesterase 1 (protein) DNA (5'-D(PAPAPTPGPCPGPCPAPTPTP*A)-3') (nucleic acid)

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.

1JY1 | pdb_00001jy1

CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)

1MU7 | pdb_00001mu7

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Tungstate Complex

1MU9 | pdb_00001mu9

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex

1NOP | pdb_00001nop

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

1R49 | pdb_00001r49

Human topoisomerase I (Topo70) double mutant K532R/Y723F

1RFF | pdb_00001rff

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.

1RFI | pdb_00001rfi

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC

1RG1 | pdb_00001rg1

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT

1RG2 | pdb_00001rg2

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA

1RGT | pdb_00001rgt

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC

1RGU | pdb_00001rgu

The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG

1RH0 | pdb_00001rh0

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT

2B9S | pdb_00002b9s

Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex

5NW9 | pdb_00005nw9

Crystal structure of the complex of Tdp1 with duplex DNA

5NWA | pdb_00005nwa

Crystal structure of the complex of Tdp1 with duplex DNA

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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

1JY1 | pdb_00001jy1

1MU7 | pdb_00001mu7

1MU9 | pdb_00001mu9

1NOP | pdb_00001nop

1R49 | pdb_00001r49

1RFF | pdb_00001rff

1RFI | pdb_00001rfi

1RG1 | pdb_00001rg1

1RG2 | pdb_00001rg2

1RGT | pdb_00001rgt

1RGU | pdb_00001rgu

1RH0 | pdb_00001rh0

2B9S | pdb_00002b9s

5NW9 | pdb_00005nw9

5NWA | pdb_00005nwa