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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = DTP

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Search Summary

This query matches 299 Structures.

Refinements

Structure Determination Methodology

experimental (299)

Scientific Name of Source Organism

	Homo sapiens (150)
	synthetic construct (63)
	Escherichia phage RB69 (16)
	Human immunodeficiency virus 1 (13)
	Saccharomyces cerevisiae (13)
	Saccharolobus solfataricus P2 (10)
	Escherichia coli K-12 (9)
	Mycolicibacterium smegmatis MC2 155 (7)
	Escherichia coli (5)
	Geobacillus stearothermophilus (5)

More...

Taxonomy

	Eukaryota (176)
	Bacteria (65)
	other sequences (63)
	Duplodnaviria (22)
	Archaea (21)
	Riboviria (16)

Experimental Method

	X-RAY DIFFRACTION (257)
	ELECTRON MICROSCOPY (42)

Polymer Entity Type

	Protein (299)
	DNA (188)
	NA-hybrid (7)
	RNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (89)
	2.0 - 2.5 (72)
	2.5 - 3.0 (79)
	3.0 - 3.5 (35)
	3.5 - 4.0 (9)
	4.0 - 4.5 (5)
	> 4.5 (5)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (13)
	2000 - 2004 (5)
	2005 - 2009 (29)
	2010 - 2014 (73)
	2015 - 2019 (90)
	2020 - 2024 (80)
	2025 - 2029 (8)

Enzyme Classification Name

	Transferases (195)
	Hydrolases (81)
	Lyases (24)
	Oxidoreductases (30)
	Ligases (2)
	Isomerases (1)

Symmetry Type

	Asymmetric (215)
	Cyclic (40)
	Dihedral (46)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (33)
	All alpha proteins (22)
	Alpha and beta proteins (a+b) (38)
	Multi-domain proteins (alpha and beta) (31)
	Artifacts (3)

AllSelected

1 to 25 of 299 Structures

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1BPE \| pdb_00001bpe	Download File View File

CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON POLYMERASE MECHANISM

Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H., Kraut, J.

(1994) Science 264: 1930-1935

Released	1994-07-31
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Rattus norvegicus
Macromolecule	DNA POLYMERASE BETA (protein)
Unique Ligands	DTP

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1CR2 \| pdb_00001cr2	Download File View File

CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DATP

Sawaya, M.R., Guo, S., Tabor, S., Richardson, C.C., Ellenberger, T.

(1999) Cell 99: 167-177

Released	1999-11-10
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia phage T7
Macromolecule	DNA PRIMASE/HELICASE (protein)
Unique Ligands	DTP, SO4

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1H7A \| pdb_00001h7a	Download File View File

Structural basis for allosteric substrate specificity regulation in class III ribonucleotide reductases: NRDD in complex with dATP

Larsson, K.-M., Andersson, J., Sjoeberg, B.-M., Nordlund, P., Logan, D.T.

(2001) Structure 9: 739

Released	2002-03-28
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Tequatrovirus T4
Macromolecule	ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN (protein)
Unique Ligands	DTP, FE2, MG

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1MO6 \| pdb_00001mo6	Download File View File

RECA-DATP-MG COMPLEX

Datta, S., Ganesh, N., Chandra, N.R., TB Structural Genomics Consortium (TBSGC)

(2003) Proteins 50: 474-485

Released	2003-02-18
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	RecA (protein)
Unique Ligands	DTP

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1PEU \| pdb_00001peu	Download File View File

Ribonucleotide Reductase Protein R1E from Salmonella typhimurium

Uppsten, M., Farnegardh, M., Jordan, A., Eliasson, R., Eklund, H., Uhlin, U.

(2003) J Mol Biology 330: 87-97

Released	2004-05-25
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Ribonucleoside-diphosphate reductase 2 alpha chain (protein)
Unique Ligands	DTP, MG

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1S0M \| pdb_00001s0m	Download File View File

Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a DNA polymerase

Ling, H., Sayer, J.M., Boudsocq, F., Plosky, B.S., Woodgate, R., Yang, W.

(2004) Proc Natl Acad Sci U S A 101: 2265-2269

Released	2004-03-30
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPT)-3' (nucleic acid) 5'-D(PAPTPAPAPAPTPCPCPTPTPCPCPCPCPCP*A)-3' (nucleic acid)
Unique Ligands	BAP, CA, DTP, MG

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1UBG \| pdb_00001ubg	Download File View File

MsREcA-dATP complex

Datta, S., Krishna, R., Ganesh, N., Chandra, N.R., Muniyappa, K., Vijayan, M.

(2003) J Bacteriol 185: 4280-4284

Released	2003-07-22
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Mycolicibacterium smegmatis
Macromolecule	RecA (protein)
Unique Ligands	DTP

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1XJF \| pdb_00001xjf	Download File View File

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex

Larsson, K.-M., Jordan, A., Eliasson, R., Reichard, P., Logan, D.T., Nordlund, P.

(2004) Nat Struct Mol Biol 11: 1142-1149

Released	2005-12-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermotoga maritima
Macromolecule	ribonucleotide reductase, B12-dependent (protein)
Unique Ligands	DTP, MG

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1XJG \| pdb_00001xjg	Download File View File

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-UDP complex

Larsson, K.-M., Jordan, A., Eliasson, R., Reichard, P., Logan, D.T., Nordlund, P.

(2004) Nat Struct Mol Biol 11: 1142-1149

Released	2005-12-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermotoga maritima
Macromolecule	ribonucleotide reductase, B12-dependent (protein)
Unique Ligands	DTP, MG, UDP

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1XJN \| pdb_00001xjn	Download File View File

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-CDP complex

Larsson, K.-M., Jordan, A., Eliasson, R., Reichard, P., Logan, D.T., Nordlund, P.

(2004) Nat Struct Mol Biol 11: 1142-1149

Released	2005-12-06
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Thermotoga maritima
Macromolecule	ribonucleotide reductase, B12-dependent (protein)
Unique Ligands	CDP, CL, DTP

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2AGQ \| pdb_00002agq	Download File View File

Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis

Ling, H., Yang, W.

(2005) EMBO J 24: 2957-2967

Released	2005-09-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPCPTPAPCPAPGPGPAPCPTP(DOC))-3' (nucleic acid) 5'-D(TPCPAPTPGPAPGPTPCPCPTPGPTPAPGPCPC)-3' (nucleic acid)
Unique Ligands	CA, DTP, MG

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2BQR \| pdb_00002bqr	Download File View File

DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine

Irimia, A., Loukachevitch, L.V., Egli, M.

(2005) J Biological Chem 280: 29750

Released	2005-06-23
Method	X-RAY DIFFRACTION 2.37 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPC)-3' (nucleic acid) 5'-D(TPCPAPTPGNEPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DTP

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2C2D \| pdb_00002c2d	Download File View File

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

Irimia, A., Loukachevitch, L.V., Egli, M.

(2006) J Biological Chem 281: 2358

Released	2005-11-29
Method	X-RAY DIFFRACTION 2.57 Å
Organisms	Saccharolobus solfataricus P2 synthetic construct
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPC)-3' (nucleic acid) 5'-D(TPCPAPC 8OGPGPAPAPTPCPCP TPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	CA, DTP

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2FAR \| pdb_00002far	Download File View File

Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese

Zhu, H., Nandakumar, J., Aniukwu, J., Wang, L.K., Glickman, M.S., Lima, C.D., Shuman, S.

(2006) Proc Natl Acad Sci U S A 103: 1711-1716

Released	2006-05-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	probable ATP-dependent DNA ligase (protein)
Unique Ligands	DTP, MN, SO4

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2G88 \| pdb_00002g88	Download File View File

MSRECA-dATP COMPLEX

Krishna, R., Manjunath, G.P., Kumar, P., Surolia, A., Chandra, N.R., Muniyappa, K., Vijayan, M.

(2006) Nucleic Acids Res 34: 2186-2195

Released	2006-05-16
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Mycolicibacterium smegmatis
Macromolecule	Protein recA (protein)
Unique Ligands	CIT, DTP, MG

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2J6S \| pdb_00002j6s	Download File View File

Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.

Irimia, A., Eoff, R.L., Guengerich, F.P., Egli, M.

(2007) J Biological Chem 282: 1456

Released	2006-11-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPC)-3' (nucleic acid) 5'-D(TPCPAPTPXPGPAPAPTPCP CPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	CA, DTP

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2J6T \| pdb_00002j6t	Download File View File

Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.

Irimia, A., Eoff, R.L., Guengerich, F.P., Egli, M.

(2007) J Biological Chem 282: 1456

Released	2006-11-22
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPC)-3' (nucleic acid) 5'-D(TPCPAPTPXPGPAPAPTPCP CPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DTP

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2JAS \| pdb_00002jas	Download File View File

Structure of deoxyadenosine kinase from M.mycoides with bound dATP

Welin, M., Wang, L., Eriksson, S., Eklund, H.

(2007) J Mol Biology 366: 1615

Released	2007-01-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mycoplasma mycoides subsp. mycoides SC
Macromolecule	DEOXYGUANOSINE KINASE (protein)
Unique Ligands	DTP, MG

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2OCP \| pdb_00002ocp	Download File View File

Crystal Structure of Human Deoxyguanosine Kinase

Johansson, K., Ramaswamy, S., Ljungkrantz, C., Knecht, W., Piskur, J., Munch-Petersen, B., Eriksson, S., Eklund, H.

(2001) Nat Struct Biol 8: 616

Released	2007-01-16
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Deoxyguanosine kinase (protein)
Unique Ligands	DTP

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2ODN \| pdb_00002odn	Download File View File

MSRECA-dATP complex

Krishna, R., Rajan Prabu, J., Manjunath, G.P., Datta, S., Chandra, N.R., Muniyappa, K., Vijayan, M.

(2007) J Mol Biology 367: 1130-1144

Released	2007-06-19
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Mycolicibacterium smegmatis
Macromolecule	Protein recA (protein)
Unique Ligands	DTP

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2OZS \| pdb_00002ozs	Download File View File

Crystal structure of RB69 gp43 in complex with DNA with dATP opposite dTMP

Zahn, K.E., Belrhali, H., Wallace, S.S., Doublie, S.

(2007) Biochemistry 46: 10551-10561

Released	2007-10-23
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Escherichia phage RB69
Macromolecule	DNA polymerase (protein) Primer DNA (nucleic acid) Template DNA (nucleic acid)
Unique Ligands	DTP, MG

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2R8I \| pdb_00002r8i	Download File View File

Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2-Propanodeoxyguanosine (PdG) by the Sulfolobus solfataricus DNA Polymerase Dpo4 Polymerase

Wang, Y., Saleh, S., Marnette, L.J., Egli, M., Stone, M.P.

(2008) Biochemistry 47: 7322-7334

Released	2008-07-22
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) DNA (5'-D(DGPDGPDGPDGPDGPDAPDAPDGPDGPDAPDTPDTPDC)-3') (nucleic acid) DNA (5'-D(DTPDCPDAPDTP(P)PDGPDAPDAPDTPDCPDCPDTPDTPDCPDCPDCPDCP*DC)-3') (nucleic acid)
Unique Ligands	CA, DTP

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2R8K \| pdb_00002r8k	Download File View File

Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin containing DNA

Carell, T., Alt, A., Lammens, K.

(2007) Science 318: 967-970

Released	2007-12-11
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA polymerase eta (protein) 5'-D(DGPDTPDGPDGPDTPDGPDAPDGPDC)-3' (nucleic acid) 5'-D(PDGPDGPDCPDTPDCPDAPDCPDCPDAP*DC)-3' (nucleic acid)
Unique Ligands	CA, CPT, DTP

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2W7P \| pdb_00002w7p	Download File View File

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct

Irimia, A., Egli, M.

(2009) J Biological Chem 284: 22467

Released	2009-06-16
Method	X-RAY DIFFRACTION 3.71 Å
Organisms	Homo sapiens
Macromolecule	DNA POLYMERASE KAPPA (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPC)-3' (nucleic acid) 5'-D(TPCPAPCP8OGPGPAPAPTPCPCPTP* TPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DTP

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2WGH \| pdb_00002wgh	Download File View File

Human Ribonucleotide reductase R1 subunit (RRM1) in complex with dATP and Mg.

Welin, R.M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kragh-Nielsen, T., Kotzsch, A., Kotenyova, T., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wisniewska, M., Nordlund, P.

(2011) Nat Struct Mol Biol 18: 316

Released	2009-05-05
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT (protein)
Unique Ligands	DTP, GOL, MG

1 to 25 of 299 Structures

Page 1 of 12

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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

1BPE | pdb_00001bpe

1CR2 | pdb_00001cr2

1H7A | pdb_00001h7a

1MO6 | pdb_00001mo6

1PEU | pdb_00001peu

1S0M | pdb_00001s0m

1UBG | pdb_00001ubg

1XJF | pdb_00001xjf

1XJG | pdb_00001xjg

1XJN | pdb_00001xjn

2AGQ | pdb_00002agq

2BQR | pdb_00002bqr

2C2D | pdb_00002c2d

2FAR | pdb_00002far

2G88 | pdb_00002g88

2J6S | pdb_00002j6s

2J6T | pdb_00002j6t

2JAS | pdb_00002jas

2OCP | pdb_00002ocp

2ODN | pdb_00002odn

2OZS | pdb_00002ozs

2R8I | pdb_00002r8i

2R8K | pdb_00002r8k

2W7P | pdb_00002w7p

2WGH | pdb_00002wgh