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232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = D3T

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Search Summary

This query matches 23 Structures.

Refinements

Structure Determination Methodology

experimental (23)

Scientific Name of Source Organism

	Homo sapiens (7)
	synthetic construct (6)
	Monkeypox virus (3)
	Escherichia coli (2)
	Escherichia phage T7 (2)
	Geobacillus kaustophilus HTA426 (2)
	Geobacillus stearothermophilus (2)
	Leishmania infantum (2)
	Mus musculus (2)
	Geobacillus kaustophilus (1)

More...

Taxonomy

	Eukaryota (13)
	Bacteria (7)
	other sequences (6)
	Varidnaviria (3)
	Duplodnaviria (2)

Experimental Method

	X-RAY DIFFRACTION (18)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

	DNA (23)
	Protein (23)

Refinement Resolution (Å)

	1.5 - 2.0 (9)
	2.0 - 2.5 (4)
	2.5 - 3.0 (6)
	3.0 - 3.5 (4)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (7)
	2010 - 2014 (9)
	2020 - 2024 (5)

Enzyme Classification Name

	Transferases (23)
	Hydrolases (8)
	Lyases (8)

Symmetry Type

Asymmetric (23)

SCOP Classification

	All alpha proteins (6)
	Alpha and beta proteins (a/b) (5)
	Alpha and beta proteins (a+b) (6)
	Multi-domain proteins (alpha and beta) (5)

AllSelected

1 to 23 of 23 Structures

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1TK8	Download File View File

T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site

Brieba, L.G., Eichman, B.F., Kokoska, R.J., Doublie, S., Kunkel, T.A., Ellenberger, T.

(2004) EMBO J 23: 3452-3461

Released	2004-08-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli Escherichia phage T7
Macromolecule	DNA polymerase (protein) Thioredoxin 1 (protein) 5'-D(CPCPCPAP(8OG)PTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPTPCPG)-3' (nucleic acid) 5'-D(CPGPAPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPAP(2DA))-3' (nucleic acid)
Unique Ligands	1PE, D3T, MES, MG, SO4

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1TKD	Download File View File

T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site

Brieba, L.G., Eichman, B.F., Kokoska, R.J., Doublie, S., Kunkel, T.A., Ellenberger, T.

(2004) EMBO J 23: 3452-3461

Released	2004-08-31
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Escherichia coli Escherichia phage T7
Macromolecule	DNA polymerase (protein) Thioredoxin 1 (protein) DNA (5'-D(CPCPCPAP(8OG)PTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPTPCPG)-3') (nucleic acid) DNA (5'-D(CPGPAPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPAP(DOC))-3') (nucleic acid)
Unique Ligands	1PE, D3T, MES, MG, SO4

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1XSN	Download File View File

Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

(2005) Nat Struct Mol Biol 12: 97-98

Released	2005-01-18
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAP(2DT))-3' (nucleic acid) 5'-D(CPGPGPCPAPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCP*G)-3' (nucleic acid)
Unique Ligands	D3T, EDO, MG, NA

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2HHW	Download File View File

ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation

Warren, J.J., Forsberg, L.J., Beese, L.S.

(2006) Proc Natl Acad Sci U S A 103: 19701-19706

Released	2006-12-12
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA Polymerase I (protein) 5'-D(CPAPTP(6OG)PCPGPAPGPTPCPAPGPG)-3' (nucleic acid) 5'-D(CPCPTPGPAPCPTPCP(DDG))-3' (nucleic acid)
Unique Ligands	D3T, MN, SO4
Unique branched monosaccharides	FRU, GLC

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2IHM	Download File View File

Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide

Moon, A.F., Pedersen, L.C., Kunkel, T.A.

(2007) Nat Struct Mol Biol 14: 45-53

Released	2006-12-12
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	DNA polymerase mu (protein) 5'-D(CPAPGPTPAPT)-3' (nucleic acid) 5'-D(CPGPGPCPAPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCP*G)-3' (nucleic acid)
Unique Ligands	D3T, MG, NA

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3C5G	Download File View File

Structure of a ternary complex of the R517K Pol lambda mutant

Garcia-Diaz, M., Bebenek, K., Foley, M.C., Pedersen, L.C., Schlick, T., Kunkel, T.A.

(2008) EMBO Rep 9: 459-464

Released	2008-07-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(DCPDAPDGPDTPDAP(2DT))-3') (nucleic acid) DNA (5'-D(DCPDGPDGPDCPDAPDAPDTPDAPDCPDTPDG)-3') (nucleic acid) DNA (5'-D(PDGPDCPDCP*DG)-3') (nucleic acid)
Unique Ligands	D3T, EDO, MG, NA

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3HP6	Download File View File

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch

Wu, E.Y., Beese, L.S.

(2011) J Biol Chem 286: 19758-19767

Released	2010-06-23
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA polymerase I, large fragment (protein) 5'-D(APCPGPCPCPGPTPGPAPTPCPG)-3' (nucleic acid) 5'-D(CPGPAPTPCPAPCPGP*(DDG))-3' (nucleic acid)
Unique Ligands	D3T, MG, SO4
Unique branched monosaccharides	FRU, GLC

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3HW8	Download File View File

ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site

Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., Pedersen, L.C., Ramsden, D.A., Kunkel, T.A.

To be published

Released	2009-08-25
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAPT)-3' (nucleic acid) 5'-D(CPGPGPCPCPAPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCPG)-3' (nucleic acid)
Unique Ligands	D3T, EDO, MG, NA

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3HWT	Download File View File

Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA

Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Pedersen, L.C., Kunkel, T.A.

To be published

Released	2009-08-25
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAP(2DT))-3' (nucleic acid) 5'-D(CPGPGPCPAPAPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCPG)-3' (nucleic acid)
Unique Ligands	D3T, EDO, MG, NA

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3HX0	Download File View File

ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA

Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., Pedersen, L.C., Ramsden, D.A., Kunkel, T.A.

To be published

Released	2009-08-25
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAPT)-3' (nucleic acid) 5'-D(CPGPGPCPAPAPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCPG)-3' (nucleic acid)
Unique Ligands	D3T, MG, NA

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3MGI	Download File View File

Ternary complex of a DNA polymerase lambda loop mutant

Garcia-Diaz, M., Bebenek, K., Zhou, R.Z., Povirk, L.F., Kunkel, T.

(2010) Nucleic Acids Res 38: 5419-5431

Released	2010-05-19
Method	X-RAY DIFFRACTION 2.603 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) DNA (nucleic acid) DNA (5'-D(CPAPGPTPAPT)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	D3T, MG, NA

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3PV8	Download File View File

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation

Wang, W., Beese, L.S.

(2011) Proc Natl Acad Sci U S A 108: 17644-17648

Released	2011-10-19
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Geobacillus kaustophilus
Macromolecule	DNA polymerase I (protein) DNA (5'-D(CAPTPAPAPGPAPGPTPCPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPGPAPCPTPCP(2DT))-3') (nucleic acid)
Unique Ligands	D3T, MG, SO4

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3UXP	Download File View File

Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP

Gridley, C.L., Jaeger, J.

(2013) Biochemistry 52: 4422-4432

Released	2012-12-05
Method	X-RAY DIFFRACTION 2.723 Å
Organisms	Rattus norvegicus
Macromolecule	DNA polymerase beta (protein) DNA 5'-D(PAPCPTPCPAPCPAPTPA)-3' (nucleic acid) DNA 5'-D(PAPTPGPTPGPAPG)-3' (nucleic acid)
Unique Ligands	D3T, NA

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4EZ9	Download File View File

Bacillus DNA Polymerase I Large Fragment Complex 2

Wang, W., Beese, L.S.

To be published

Released	2013-07-24
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Geobacillus kaustophilus HTA426
Macromolecule	DNA polymerase (protein) DNA (5'-D(CPAPTPTPAPGPAPGPTPCPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPGPAPCPTPCP(2DT))-3') (nucleic acid)
Unique Ligands	D3T, MPD, SO4

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4F3O	Download File View File

DNA Polymerase I Large Fragment Complex 5

Wang, W., Beese, L.S.

To be published

Released	2013-07-24
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Geobacillus kaustophilus HTA426 synthetic construct
Macromolecule	DNA polymerase (protein) DNA (5'-D(CAPTPGPAPGPAPGPTPCPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPGPAPCPTPCP(2DT))-3') (nucleic acid)
Unique Ligands	D3T, MN, MPD, SO4

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4I27	Download File View File

Ternary complex of mouse TdT with ssDNA and incoming nucleotide

Gouge, J., Delarue, M.

(2013) J Mol Biol 425: 4334-4352

Released	2013-07-24
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	DNA nucleotidylexotransferase (protein) 5'-D(APAPAPAPAPT)-3' (nucleic acid)
Unique Ligands	D3T, MG, NA

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4P4M	Download File View File

Crystal structure of Leishmania infantum polymerase beta: Ternary P/T complex

Mejia, E., Burak, M., Alonso, A., Larraga, V., Kunkel, T.A., Bebenek, K., Garcia-Diaz, M.

(2014) DNA Repair (Amst) 18: 1-9

Released	2014-08-06
Method	X-RAY DIFFRACTION 1.9185 Å
Organisms	Leishmania infantum synthetic construct
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPAPGPTPA)-3') (nucleic acid) DNA (5'-D(PAPTPAPCPTP*G)-3') (nucleic acid)
Unique Ligands	D3T, MG, NA

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4P4O	Download File View File

Crystal structure of Leishmania infantum polymerase beta: Ternary gap complex

Mejia, E., Burak, M., Alonso, A., Larraga, V., Kunkel, T., Bebenek, K., Garcia-Diaz, M.

(2014) DNA Repair (Amst) 18: 1-9

Released	2014-08-06
Method	X-RAY DIFFRACTION 2.3001 Å
Organisms	Leishmania infantum synthetic construct
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPAPGPTPAPT)-3') (nucleic acid) DNA (5'-D(PCPGPGPCPAPAPTPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCP*G)-3') (nucleic acid)
Unique Ligands	D3T, MG, NA

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7KC0	Download File View File

Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp

Zheng, F., Georgescu, R., Li, H., O'Donnell, M.E.

(2020) Proc Natl Acad Sci U S A 117: 30344-30353

Released	2020-12-02
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	D3T, MG, SF4, ZN

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8V5R	Download File View File

Active conformation of DNA polymerase gamma bound to DNA

Riccio, A.A., Krahn, J.M., Bouvette, J., Borgnia, J.M., Copeland, W.C.

(2024) Nucleic Acids Res 52: 7863-7875

Released	2024-07-10
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase subunit gamma-1 (protein) DNA polymerase subunit gamma-2, mitochondrial (protein) Template DNA (nucleic acid) primer DNA (nucleic acid)
Unique Ligands	D3T, MG

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8WPE	Download File View File

Structure of monkeypox virus polymerase complex F8-A22-E4-H5 (tag-free A22) with exogenous DNA

Wang, X., Li, N., Gao, N.

(2023) Mol Cell 83: 4398

Released	2023-11-29
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Monkeypox virus synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	D3T, MG

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8WPF	Download File View File

Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with exogenous DNA bearing one abasic site

Wang, X., Li, N., Gao, N.

(2023) Mol Cell 83: 4398

Released	2023-11-29
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Monkeypox virus synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	D3T, MG

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8WPK	Download File View File

Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with exgenous DNA

Wang, X., Li, N., Gao, N.

(2023) Mol Cell 83: 4398

Released	2023-11-29
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Monkeypox virus synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	D3T, MG

1 to 23 of 23 Structures

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