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228,227 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Prakash, L."

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Search Summary

This query matches 25 Structures.

Refinements

Structure Determination Methodology

experimental (25)

Scientific Name of Source Organism

	Homo sapiens (16)
	Saccharomyces cerevisiae (7)
	Saccharolobus solfataricus (2)

Taxonomy

	Eukaryota (23)
	Archaea (2)

Experimental Method

X-RAY DIFFRACTION (25)

Polymer Entity Type

	Protein (25)
	DNA (22)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (15)
	2.5 - 3.0 (7)
	3.0 - 3.5 (2)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (4)
	2005 - 2009 (13)
	2010 - 2014 (6)
	2015 - 2019 (1)

Enzyme Classification Name

	Transferases (25)
	Hydrolases (1)
	Ligases (1)

Symmetry Type

	Asymmetric (18)
	Cyclic (7)

SCOP Classification

	Alpha and beta proteins (a+b) (16)
	Multi-domain proteins (alpha and beta) (15)

AllSelected

1 to 25 of 25 Structures

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1AYZ	Download File View File

CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION

Worthylake, D.K., Prakash, S., Prakash, L., Hill, C.P.

(1998) J Biol Chem 273: 6271-6276

Released	1998-08-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	UBIQUITIN-CONJUGATING ENZYME RAD6 (protein)

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1JIH	Download File View File

Yeast DNA Polymerase ETA

Trincao, J., Johnson, R.E., Escalante, C.R., Prakash, S., Prakash, L., Aggarwal, A.K.

(2001) Mol Cell 8: 417-426

Released	2002-01-09
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA Polymerase ETA (protein)

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1S97	Download File View File

DPO4 with GT mismatch

Trincao, J., Johnson, R.E., Wolfle, W.T., Escalante, C.R., Prakash, S., Prakash, L., Aggarwal, A.K.

(2004) Nat Struct Mol Biol 11: 457-462

Released	2004-04-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPCPTPG)-3' (nucleic acid) 5'-D(TTPCPAPGPTPAPGPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DCT

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1S9F	Download File View File

DPO with AT matched

Trincao, J., Johnson, R.E., Wolfle, W.T., Escalante, C.R., Prakash, S., Prakash, L., Aggarwal, A.K.

(2004) Nat Struct Mol Biol 11: 457-462

Released	2005-02-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPCPTPA)-3' (nucleic acid) 5'-D(TTPCPAPGPTPAPGPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DDY, MG

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1T3N	Download File View File

Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP

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

(2004) Nature 430: 377-380

Released	2004-07-20
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	polymerase (DNA directed) iota (protein) Primer DNA strand (nucleic acid) Template DNA strand (nucleic acid)
Unique Ligands	MG, TTP

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1T94	Download File View File

Crystal structure of the catalytic core of human DNA polymerase kappa

Uljon, S.N., Johnson, R.E., Edwards, T.A., Prakash, S., Prakash, L., Aggarwal, A.K.

(2004) Structure 12: 1395-1404

Released	2004-08-31
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	polymerase (DNA directed) kappa (protein)

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2ALZ	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	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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2DPI	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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2DPJ	Download File View File

structure of hPoli with DNA and dTTP

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	MG, TTP

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2FLL	Download File View File

Ternary complex of human DNA polymerase iota with DNA and dTTP

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

(2006) Structure 14: 749-755

Released	2006-12-12
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) DNA primer strand (nucleic acid) DNA template strand (nucleic acid)
Unique Ligands	MG, TTP

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2FLN	Download File View File

binary complex of catalytic core of human DNA polymerase iota with DNA (template A)

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

(2006) Structure 14: 749-755

Released	2006-12-05
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) DNA primer strand (nucleic acid) DNA template strand (nucleic acid)

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2FLP	Download File View File

Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)

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

(2006) Structure 14: 749-755

Released	2006-12-05
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) DNA primer strand (nucleic acid) DNA template strand (nucleic acid)

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2OH2	Download File View File

Ternary Complex of Human DNA Polymerase

Lone, S., Townson, S.A., Uljon, S.N., Prakash, S., Prakash, L., Aggarwal, A.K.

To be published

Released	2007-02-27
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase kappa (protein) 5'-D(GPGPGGPGPAPAPGPGPAPCPCPC)-3' (nucleic acid) 5'-D(TPTCPCPAPGPGPGPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	MG, TTP

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3BJY	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

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3H40	Download File View File

Binary complex of human DNA polymerase iota with template U/T

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

(2009) Structure 17: 974-980

Released	2009-07-21
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(BRU)PGPGPGPTPCPCPT)-3' (nucleic acid)
Unique Ligands	SO4

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3H4B	Download File View File

Ternary complex of human DNA polymerase iota with template U/T and incoming dATP

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

(2009) Structure 17: 974-980

Released	2009-07-21
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) 5'-D(APGPGPAPCPCP(DOC))-3' (nucleic acid) 5'-D(TP(BRU)PGPGPGPTPCPCPT)-3' (nucleic acid)
Unique Ligands	DTP, MG

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3H4D	Download File View File

Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP

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

(2009) Structure 17: 974-980

Released	2009-07-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase iota (protein) 5'-D(APGPGPAPCPCP(DOC)) (nucleic acid) 5'-D(TP(BRU)PGPGPGPTPCPCPT) (nucleic acid)
Unique Ligands	DGT, MG

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3MFH	Download File View File

DNA Polymerase Eta in Complex With Undamaged DNA

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

(2010) Nature 465: 1039-1043

Released	2010-06-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA polymerase eta (protein) 5'-D(GPTPCPCPTPCPCPCPCPTP(DOC))-3' (nucleic acid) 5'-D(TPAPAPTPTPGPAPGPGPGPGPAPGPGPAP*C)-3' (nucleic acid)
Unique Ligands	DTP, MG, SO4

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3MFI	Download File View File

DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer

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

(2010) Nature 465: 1039-1043

Released	2010-06-23
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA polymerase eta (protein) 5'-D(GPTPCPCPTPCPCPCPCPTP(DOC))-3' (nucleic acid) 5'-D(TPAPAP(TTD)PGPAPGPGPGPGPAPGPGPAPC)-3' (nucleic acid)
Unique Ligands	DTP, MG, SO4

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3PZP	Download File View File

Human DNA polymerase kappa extending opposite a cis-syn thymine dimer

Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.

(2011) J Mol Biol 408: 252-261

Released	2011-12-28
Method	X-RAY DIFFRACTION 3.336 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase kappa (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPCPCPA)-3' (nucleic acid) 5'-D(TPTPCPCP(TTD)PGPGPTPCPCPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	DTP, MG

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3TQ1	Download File View File

Human DNA Polymerase eta in binary complex with DNA

Ummat, A., Silverstein, T.D., Jain, R., Buku, A., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2012) J Mol Biol 415: 627-634

Released	2012-02-08
Method	X-RAY DIFFRACTION 2.556 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) DNA (5'-D(TPAPGPCPGPTPCPAPT)-3') (nucleic acid) DNA (5'-D(TPCPAPTPTPAPTPGPAPCPGPCPT)-3') (nucleic acid)

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4EEY	Download File View File

Crystal structure of human DNA polymerase eta in ternary complex with a cisplatin DNA adduct

Ummat, A., Rechkoblit, O., Jain, R., Choudhury, J.R., Johnson, R.E., Silverstein, T.D., Buku, A., Lone, S., Prakash, L., Prakash, S., Aggarwal, A.K.

(2012) Nat Struct Mol Biol 19: 628-632

Released	2012-05-09
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase eta (protein) 5'-D(CPTPTPGPGPTPCPTPCPCPTPCPC)-3' (nucleic acid) 5'-D(TPGPGPAPGPGPAPGPA)-3' (nucleic acid)
Unique Ligands	CPT, DCP, MG

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4PTF	Download File View File

Ternary crystal structure of yeast DNA polymerase epsilon with template G

Jain, R., Rajashankar, K.R., Buku, A., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2014) PLoS One 9: e94835-e94835

Released	2014-04-30
Method	X-RAY DIFFRACTION 2.809 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DNA polymerase epsilon catalytic subunit A (protein) 5'-D(APTPCPCPTPCPCPCPCPTPAP(DOC))-3' (nucleic acid) 5'-D(TPAPAPGPGPTPAPGPGPGPGPAPGPGPAPT)-3' (nucleic acid)
Unique Ligands	CA, DCP, EDO, NA

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5L2X	Download File View File

Crystal structure of human PrimPol ternary complex

Rechkoblit, O., Gupta, Y.K., Malik, R., Rajashankar, K.R., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2016) Sci Adv 2: e1601317-e1601317

Released	2016-11-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed primase/polymerase protein (protein) DNA (5'-D(PGPGPTPAPGPCP(DDG))-3') (nucleic acid) DNA (5'-D(PTPCPGPCP(5IU)PAPCP*C)-3') (nucleic acid)
Unique Ligands	CA, DTP