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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) = DCP

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Search Summary

This query matches 177 Structures.

Refinements

Structure Determination Methodology

experimental (177)

Scientific Name of Source Organism

	Homo sapiens (81)
	synthetic construct (62)
	Saccharomyces cerevisiae (17)
	Escherichia phage RB69 (16)
	Saccharolobus solfataricus P2 (14)
	Geobacillus stearothermophilus (5)
	Human immunodeficiency virus 1 (5)
	Saccharolobus solfataricus (5)
	Saccharomyces cerevisiae S288C (5)
	Escherichia coli K-12 (4)

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Taxonomy

	Eukaryota (105)
	other sequences (62)
	Bacteria (24)
	Archaea (21)
	Duplodnaviria (18)
	Riboviria (7)
	Varidnaviria (3)
	unclassified sequences (3)

Experimental Method

	X-RAY DIFFRACTION (160)
	ELECTRON MICROSCOPY (17)

Polymer Entity Type

	Protein (177)
	DNA (143)
	RNA (4)
	NA-hybrid (3)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (48)
	2.0 - 2.5 (59)
	2.5 - 3.0 (48)
	3.0 - 3.5 (18)
	3.5 - 4.0 (2)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (10)
	2005 - 2009 (17)
	2010 - 2014 (60)
	2015 - 2019 (37)
	2020 - 2024 (47)
	2025 - 2029 (1)

Enzyme Classification Name

	Transferases (152)
	Lyases (41)
	Hydrolases (52)
	Oxidoreductases (2)
	Isomerases (1)
	Ligases (1)

Symmetry Type

	Asymmetric (150)
	Dihedral (19)
	Cyclic (10)

SCOP Classification

	Multi-domain proteins (alpha and beta) (37)
	Alpha and beta proteins (a+b) (32)
	Alpha and beta proteins (a/b) (28)
	All alpha proteins (15)
	Artifacts (7)
	All beta proteins (2)
	Small proteins (2)

AllSelected

1 to 25 of 177 Structures

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1H78 \| pdb_00001h78	Download File View File

STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP.

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

(2001) Structure 9: 739

Released	2002-07-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Tequatrovirus T4
Macromolecule	ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN (protein)
Unique Ligands	DCP, MG

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1LV5 \| pdb_00001lv5	Download File View File

Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP

Johnson, S.J., Taylor, J.S., Beese, L.S.

(2003) Proc Natl Acad Sci U S A 100: 3895-3900

Released	2003-03-25
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA POLYMERASE I (protein) 5'-D(APCPGPTPCPGPCPTPGPAPTPCPCPG)-3' (nucleic acid) 5'-D(GPGPAPTPCPAPGPCPGPA)-3' (nucleic acid)
Unique Ligands	DCP, MG, MN, SO4

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1MQ3 \| pdb_00001mq3	Download File View File

Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine Template Paired with dCTP

Krahn, J.M., Beard, W.A., Miller, H., Grollman, A.P., Wilson, S.H.

(2003) Structure 11: 121-127

Released	2003-01-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	DNA POLYMERASE BETA (protein) 5'-D(CPCPGPAPCP(8OG)PGPCPGPCPAPTPCPAPGPC)-3' (nucleic acid) 5'-D(GPCPTPGPAPTPGPCPGP(DOC))-3' (nucleic acid) 5'-D(PGPTPCPGP*G)-3' (nucleic acid)
Unique Ligands	DCP, MG, NA

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1NKE \| pdb_00001nke	Download File View File

A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A CYTOSINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP.

Johnson, S.J., Beese, L.S.

(2004) Cell 116: 803-816

Released	2004-03-30
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA POLYMERASE I (protein) DNA PRIMER STRAND (nucleic acid) DNA TEMPLATE STRAND (nucleic acid)
Unique Ligands	DCP, MG, SO4
Unique branched monosaccharides	FRU, GLC

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1PEO \| pdb_00001peo	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 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Ribonucleoside-diphosphate reductase 2 alpha chain (protein)
Unique Ligands	DCP, MG

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1PKK \| pdb_00001pkk	Download File View File

Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii

Huffman, J.L., Li, H., White, R.H., Tainer, J.A.

(2003) J Mol Biology 331: 885-896

Released	2003-09-23
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Bifunctional deaminase/diphosphatase (protein)
Unique Ligands	DCP, EDO

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1Q9Y \| pdb_00001q9y	Download File View File

CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA

Freisinger, E., Grollman, A.P., Miller, H., Kisker, C.

(2004) EMBO J 23: 1494-1505

Released	2004-04-27
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia phage RB69
Macromolecule	DNA POLYMERASE (protein) 5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3' (nucleic acid) 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3' (nucleic acid)
Unique Ligands	CA, DCP

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1S0N \| pdb_00001s0n	Download File View File

Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift

Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

(2004) Mol Cell 13: 751-762

Released	2004-03-30
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPCPAPCPTPGPAPTPCPAPCPG)-3' (nucleic acid) 5'-D(TPAPCPGPAPCPGPTPGPAPTPCPAPGPTPGPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DCP

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1S10 \| pdb_00001s10	Download File View File

Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift

Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

(2004) Mol Cell 13: 751-762

Released	2004-03-30
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPCPTPA)-3' (nucleic acid) 5'-D(TPCPAPGPTPAPGPTPCPCPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	CA, DCP

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1XS4 \| pdb_00001xs4	Download File View File

dCTP deaminase from Escherichia coli- E138A mutant enzyme in complex with dCTP

Johansson, E., Fano, M., Bynck, J.H., Neuhard, J., Larsen, S., Sigurskjold, B.W., Christensen, U., Willemoes, M.

(2005) J Biological Chem 280: 3051-3059

Released	2004-12-21
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Escherichia coli
Macromolecule	Deoxycytidine triphosphate deaminase (protein)
Unique Ligands	DCP, MG

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2ALZ \| pdb_00002alz	Download File View File

Ternary Complex of hPoli with DNA and dCTP

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2005) Structure 13: 1569-1577

Released	2005-10-25
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) 5'-D(APGPGPAPCPCP(DOC))-3' (nucleic acid) 5'-D(TPGPGPGPGPTPCPCPT)-3' (nucleic acid)
Unique Ligands	DCP, MG

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2AQ4 \| pdb_00002aq4	Download File View File

Ternary complex of the catalytic core of REV1 with DNA and dCTP.

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2005) Science 309: 2219-2222

Released	2005-10-04
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA repair protein REV1 (protein) 5'-D(APTPCPCPTPCPCPCPCPTPAPC)-3' (nucleic acid) 5'-D(TPAPAPGPGPTPAPGPGPGPGPAPGPGPAPT)-3' (nucleic acid)
Unique Ligands	DCP, MG

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2ASD \| pdb_00002asd	Download File View File

oxoG-modified Insertion Ternary Complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(CPTAPAPCP(8OG)PCPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAP(DDG))-3' (nucleic acid)
Unique Ligands	CA, DCP

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2ATL \| pdb_00002atl	Download File View File

Unmodified Insertion Ternary Complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Dpo4 polymerase IV (protein) 5'-D(CPTAPAPCPGPCPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAP(DDG))-3' (nucleic acid)
Unique Ligands	CA, DCP

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2C2E \| pdb_00002c2e	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 2.61 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPC)-3' (nucleic acid) 5'-D(TPCPAPC 8OGPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DCP

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2DPI \| pdb_00002dpi	Download File View File

Ternary complex of hPoli with DNA and dCTP

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2006) Nat Struct Mol Biol 13: 619-625

Released	2006-07-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) 5'-D(APGPGPAPCPCP(DOC))-3' (nucleic acid) 5'-D(TP(EDA)PGPGPGPTPCPCPT)-3' (nucleic acid)
Unique Ligands	DCP, MG

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2HHU \| pdb_00002hhu	Download File View File

C:O6-methyl-guanine in the polymerase postinsertion site (-1 basepair position)

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 1.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA Polymerase I (protein) 5'-D(GPCPGPAPTPCPAPGPCPCPC)-3' (nucleic acid) 5'-D(GPTPAPCP(6OG)PGPGPCPTPGPAPTPCPGPCP*A)-3' (nucleic acid)
Unique Ligands	DCP, MG, SO4
Unique branched monosaccharides	FRU, GLC

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2HVW \| pdb_00002hvw	Download File View File

Crystal structure of dCMP deaminase from Streptococcus mutans

Hou, H.F., Gao, Z.Q., Li, L.F., Liang, Y.H., Su, X.D., Dong, Y.H.

(2008) J Mol Biology 377: 220-231

Released	2007-09-11
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Streptococcus mutans
Macromolecule	deoxycytidylate deaminase (protein)
Unique Ligands	DCP, DDN, DIO, MG, ZN

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2JAQ \| pdb_00002jaq	Download File View File

Structure of deoxyadenosine kinase from M. mycoides with bound dCTP

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

(2007) J Mol Biology 366: 1615

Released	2007-01-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mycoplasma mycoides subsp. mycoides SC
Macromolecule	DEOXYGUANOSINE KINASE (protein)
Unique Ligands	DCP

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2PFP \| pdb_00002pfp	Download File View File

DNA Polymerase lambda in complex with DNA and dCTP

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

(2007) DNA Repair (Amst) 6: 1333-1340

Released	2007-05-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) Downstream Primer (nucleic acid) Primer (nucleic acid) Template (nucleic acid)
Unique Ligands	DCP, MG, NA

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2PFQ \| pdb_00002pfq	Download File View File

Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal

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

(2007) DNA Repair (Amst) 6: 1333-1340

Released	2007-05-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) Downstream Primer (nucleic acid) Primer (nucleic acid) Template (nucleic acid)
Unique Ligands	DCP, MG, MN, NA, PPV

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2R8J \| pdb_00002r8j	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 3.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(DGPDTPDGPDGPDAPDTPDGPDAPDG)-3') (nucleic acid) DNA (5'-D(PDGPDGPDCPDTPDCPDAPDTPDCPDCPDAPDC)-3') (nucleic acid)
Unique Ligands	CA, CPT, DCP

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2VP4 \| pdb_00002vp4	Download File View File

Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase

Mikkelsen, N.E., Munch-Petersen, B., Eklund, H.

(2008) FEBS J 275: 2151

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Drosophila melanogaster
Macromolecule	DEOXYNUCLEOSIDE KINASE (protein)
Unique Ligands	DCP

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2XCP \| pdb_00002xcp	Download File View File

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dCTP - MAGNESIUM FORM

Irimia, A., Egli, M.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1013

Released	2010-09-08
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTP TPDOC)-3' (nucleic acid) 5'-D(TPCPAPCP8OGPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	DCP, MG

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3BJY \| pdb_00003bjy	Download File View File

Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2008) Structure 16: 239-245

Released	2008-10-28
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA repair protein REV1 (protein) DNA (5'-D(DAPDTPDCPDCPDTPDCPDCPDCPDCPDTPDAP(DOC))-3') (nucleic acid) DNA (5'-D(DTPDAPDAP(P)PDGPDTPDAPDGPDGPDGPDGPDAPDGPDGPDAPDT)-3') (nucleic acid)
Unique Ligands	DCP, MG

1 to 25 of 177 Structures

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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

1H78 | pdb_00001h78

1LV5 | pdb_00001lv5

1MQ3 | pdb_00001mq3

1NKE | pdb_00001nke

1PEO | pdb_00001peo

1PKK | pdb_00001pkk

1Q9Y | pdb_00001q9y

1S0N | pdb_00001s0n

1S10 | pdb_00001s10

1XS4 | pdb_00001xs4

2ALZ | pdb_00002alz

2AQ4 | pdb_00002aq4

2ASD | pdb_00002asd

2ATL | pdb_00002atl

2C2E | pdb_00002c2e

2DPI | pdb_00002dpi

2HHU | pdb_00002hhu

2HVW | pdb_00002hvw

2JAQ | pdb_00002jaq

2PFP | pdb_00002pfp

2PFQ | pdb_00002pfq

2R8J | pdb_00002r8j

2VP4 | pdb_00002vp4

2XCP | pdb_00002xcp

3BJY | pdb_00003bjy