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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "Transferase/DNA"

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Search Summary

This query matches 1,706 Structures.

Refinements

Structure Determination Methodology

experimental (1,706)

Scientific Name of Source Organism

	Homo sapiens (720)
	synthetic construct (597)
	Escherichia phage RB69 (103)
	Geobacillus stearothermophilus (80)
	Saccharolobus solfataricus P2 (79)
	Escherichia coli (77)
	Mus musculus (69)
	Thermus aquaticus (64)
	Saccharomyces cerevisiae (54)
	Human immunodeficiency virus 1 (44)

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Taxonomy

	Eukaryota (895)
	other sequences (600)
	Bacteria (383)
	Duplodnaviria (165)
	Archaea (153)
	Riboviria (119)
	unclassified sequences (24)
	Varidnaviria (18)
	unclassified viruses (1)

Experimental Method

	X-RAY DIFFRACTION (1,543)
	ELECTRON MICROSCOPY (162)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (1,706)
	DNA (1,671)
	RNA (118)
	NA-hybrid (50)

Refinement Resolution (Å)

	1.0 - 1.5 (8)
	1.5 - 2.0 (433)
	2.0 - 2.5 (513)
	2.5 - 3.0 (387)
	3.0 - 3.5 (209)
	3.5 - 4.0 (90)
	4.0 - 4.5 (35)
	> 4.5 (30)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (128)
	2000 - 2004 (75)
	2005 - 2009 (191)
	2010 - 2014 (488)
	2015 - 2019 (427)
	2020 - 2024 (384)
	2025 - 2029 (10)

Enzyme Classification Name

	Transferases (1,641)
	Lyases (319)
	Hydrolases (233)
	Isomerases (9)
	Ligases (3)

Symmetry Type

	Asymmetric (1,566)
	Cyclic (136)
	Dihedral (4)

SCOP Classification

	Multi-domain proteins (alpha and beta) (312)
	All alpha proteins (176)
	Alpha and beta proteins (a/b) (268)
	Alpha and beta proteins (a+b) (247)
	Artifacts (32)
	All beta proteins (16)
	Low resolution protein structures (2)
	Small proteins (11)
	Designed proteins (1)
	Peptides (2)

AllSelected

1 to 25 of 1,706 Structures

Page 1 of 69

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10MH \| pdb_000010mh	Download File View File

TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DNA CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET

Sheikhnejad, G., Brank, A., Christman, J.K., Goddard, A., Alvarez, E., Ford Junior, H., Marquez, V.E., Marasco, C.J., Sufrin, J.R., O'Gara, M., Cheng, X.

(1999) J Mol Biology 285: 2021-2034

Released	1999-02-09
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Haemophilus haemolyticus
Macromolecule	PROTEIN (CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI) (protein) DNA (5'-D(PCPCPAPTPGP(5CM)PGPCPTPGPAPC)-3') (nucleic acid) DNA (5'-D(PGPTPCPAPGP5NCPGPCPAPTPGPG)-3') (nucleic acid)
Unique Ligands	SAH

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1BDX \| pdb_00001bdx	Download File View File

E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY

Hargreaves, D., Rice, D.W., Sedelnikova, S.E., Artymiuk, P.J., Lloyd, R.G., Rafferty, J.B.

(1998) Nat Struct Biol 5: 441-446

Released	1999-11-24
Method	X-RAY DIFFRACTION 6 Å
Organisms	Escherichia coli BL21(DE3)
Macromolecule	HOLLIDAY JUNCTION DNA HELICASE RUVA (protein) DNA (5'-D(PGPCPAPTPGPCPAPTPAPTPGPCPAPTPGPC)-3') (nucleic acid)

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1BPX \| pdb_00001bpx	Download File View File

DNA POLYMERASE BETA/DNA COMPLEX

Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J., Pelletier, H.

(1997) Biochemistry 36: 11205-11215

Released	1997-06-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (DNA POLYMERASE BETA) (protein) DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3') (nucleic acid) DNA (5'-D(GPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	NA

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1BPY \| pdb_00001bpy	Download File View File

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP

Sawaya, M.R., Pelletier, H., Prasad, R., Wilson, S.H., Kraut, J.

(1997) Biochemistry 36: 11205-11215

Released	1997-06-16
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	PROTEIN (DNA POLYMERASE BETA) (protein) DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPDOC)-3') (nucleic acid) DNA (5'-D(GPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	DCT, MG, NA

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1BPZ \| pdb_00001bpz	Download File View File

HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA

Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J., Pelletier, H.

(1997) Biochemistry 36: 11205-11215

Released	1997-06-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (DNA POLYMERASE BETA) (protein) DNA (5'-D(CPCPGPAPCPCPAPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPTPG)-3') (nucleic acid) DNA (5'-D(GPTPCPGPG)-3') (nucleic acid)
Unique Ligands	NA

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1CEZ \| pdb_00001cez	Download File View File

CRYSTAL STRUCTURE OF A T7 RNA POLYMERASE-T7 PROMOTER COMPLEX

Cheetham, G.M.T., Jeruzalmi, D., Steitz, T.A.

(1999) Nature 399: 80-83

Released	1999-05-21
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia phage T7
Macromolecule	PROTEIN (BACTERIOPHAGE T7 RNA POLYMERASE) (protein) DNA (5'-D(PTPAPAPTPAPCPGPAPCPTPCPAPCPTPA)-3') (nucleic acid) DNA (5'-D(PTPAPTPAPGPTPGPAPGPTPCPGPTPAPTPTPA)-3') (nucleic acid)

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1CLQ \| pdb_00001clq	Download File View File

CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX AT 2.7 A RESOLUTION

Shamoo, Y., Steitz, T.A.

(1999) Cell 99: 155-166

Released	1999-10-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia phage RB69
Macromolecule	PROTEIN (DNA POLYMERASE) (protein) DNA (5'-D(APGPTPAPGPTPTPCPCPGPCPG)-3') (nucleic acid) DNA (5'-D(GPCPGPGPAPAPCPTPAPCP*T)-3') (nucleic acid)
Unique Ligands	CA, GDP

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1D0E \| pdb_00001d0e	Download File View File

CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN

Najmudin, S., Cote, M.L., Sun, D., Yohannan, S., Montano, S.P., Gu, J., Georgiadis, M.M.

(2000) J Mol Biology 296: 613-632

Released	2000-04-04
Method	X-RAY DIFFRACTION 3 Å
Organisms	Moloney murine leukemia virus
Macromolecule	REVERSE TRANSCRIPTASE (protein) 5'-D(TPTPTPCPAPTPGPCPAPTP*G)-3' (nucleic acid)

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1D8Y \| pdb_00001d8y	Download File View File

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA

Teplova, M., Wallace, S.T., Tereshko, V., Minasov, G., Simons, A.M., Cook, P.D., Manoharan, M., Egli, M.

(1999) Proc Natl Acad Sci U S A 96: 14240-14245

Released	1999-12-02
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Escherichia coli
Macromolecule	DNA POLYMERASE I (protein) D(T)19 OLIGOMER (nucleic acid)
Unique Ligands	SO4, ZN

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1DCT \| pdb_00001dct	Download File View File

DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA

Reinisch, K.M., Chen, L., Verdine, G.L., Lipscomb, W.N.

(1995) Cell 82: 143-153

Released	1995-09-15
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Haemophilus influenzae biotype aegyptius
Macromolecule	PROTEIN (MODIFICATION METHYLASE HAEIII) (protein) DNA (5'-D(APCPCPAPGPCPAPGPGP(C49)PCPAPCPCPAPGPTPG)-3') (nucleic acid) DNA (5'-D(TPCPAPCPTPGPGPTPGPGP(C5M)PCPTPGPCPTPGPG)-3') (nucleic acid)
Unique Ligands	CA

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1FJX \| pdb_00001fjx	Download File View File

STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY

Vilkaitis, G., Dong, A., Weinhold, E., Cheng, X., Klimasauskas, S.

(2000) J Biological Chem 275: 38722-38730

Released	2000-12-15
Method	X-RAY DIFFRACTION 2.26 Å
Organisms	Haemophilus haemolyticus
Macromolecule	HHAI DNA METHYLTRANSFERASE (protein) DNA (5'-D(TPGPAPTPAPGPCPGPCPTPAPTP*C)-3') (nucleic acid)
Unique Ligands	SAH, SO4

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1G38 \| pdb_00001g38	Download File View File

ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX

Goedecke, K., Pignot, M., Goody, R.S., Scheidig, A.J., Weinhold, E.

(2001) Nat Struct Biol 8: 121-125

Released	2001-03-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus aquaticus
Macromolecule	MODIFICATION METHYLASE TAQI (protein) 5'-D(GPAPCPAPTPCPGP(6MA)PAPC)-3' (nucleic acid) 5'-D(GPTPTPCPGPAPTPGPTPC)-3' (nucleic acid)
Unique Ligands	NEA

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1HUO \| pdb_00001huo	Download File View File

CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP

Arndt, J.W., Gong, W., Zhong, X., Showalter, A.K., Liu, J., Lin, Z., Paxson, C., Tsai, M.-D., Chan, M.K.

(2001) Biochemistry 40: 5368-5375

Released	2001-04-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Rattus norvegicus
Macromolecule	DNA POLYMERASE BETA (protein) 5'-D(APAPTPAPGPGPCPGPTPCPG)-3' (nucleic acid) 5'-D(PCPGPAPCPGPCPC)-3' (nucleic acid)
Unique Ligands	CR, TTE

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1HUZ \| pdb_00001huz	Download File View File

CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP

Arndt, J.W., Gong, W., Zhong, X., Showalter, A.K., Liu, J., Lin, Z., Paxson, C., Tsai, M.-D., Chan, M.K.

(2001) Biochemistry 40: 5368-5375

Released	2001-04-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Rattus norvegicus
Macromolecule	DNA POLYMERASE BETA (protein) 5'-D(APAPTPAPGPGPCPGPTPCPG)-3' (nucleic acid) 5'-D(PCPGPAPCPGPCPCP*T)-3' (nucleic acid)
Unique Ligands	CR, MDN

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1I6J \| pdb_00001i6j	Download File View File

CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED GUANINES AND TWO G-A MISPAIRS COMPLEXED WITH THE N-TERMINAL FRAGMENT OF MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE

Cote, M.L., Georgiadis, M.M.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1238-1250

Released	2001-09-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Moloney murine leukemia virus
Macromolecule	REVERSE TRANSCRIPTASE (protein) 5'-D(APCPGPGPGPAPCPGPAPC)-3' (nucleic acid) 5'-D(GPTPCPGPTPC)-3' (nucleic acid)

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1IG9 \| pdb_00001ig9	Download File View File

Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase

Franklin, M.C., Wang, J., Steitz, T.A.

(2001) Cell 105: 657-667

Released	2001-06-11
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia phage RB69
Macromolecule	DNA POLYMERASE (protein) 5'-D(APCPAPGPGPTPAPAPGPCPAPGPTPCPCPGPCPG)-3' (nucleic acid) 5'-D(GPCPGPGPAPCPTPGPCPTPTPAPCP(DOC))-3' (nucleic acid)
Unique Ligands	CA, TTP

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1IXY \| pdb_00001ixy	Download File View File

Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex

Lariviere, L., Morera, S.

(2002) J Mol Biology 324: 483-490

Released	2002-12-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Tequatrovirus T4
Macromolecule	DNA beta-glucosyltransferase (protein) 5'-D(CPTPAPTPCPTPGPAPGPTPAPTPC)-3' (nucleic acid) 5'-D(GPAPTPAPCPTP3DRPAPGPAPTPAPG)-3' (nucleic acid)
Unique Ligands	MG, MPD, UDP

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1JX4 \| pdb_00001jx4	Download File View File

Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

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

(2001) Cell 107: 91-102

Released	2001-10-05
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (family Y) (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPCPTPA)-3' (nucleic acid) 5'-D(TTPCPAPTPTPAPGPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	ADI, CA, MG

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1JXL \| pdb_00001jxl	Download File View File

Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

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

(2001) Cell 107: 91-102

Released	2001-10-05
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (family Y) (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPT)-3' (nucleic acid) 5'-D(TTPCPGPAPAP(BRU)PCPCPTP(BRU)PCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	CA, DG3, EDO, MG

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1KDH \| pdb_00001kdh	Download File View File

Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA

Delarue, M., Boule, J.B., Lescar, J., Expert-Bezancon, N., Jourdan, N., Sukumar, N., Rougeon, F., Papanicolaou, C.

(2002) EMBO J 21: 427-439

Released	2002-05-13
Method	X-RAY DIFFRACTION 3 Å
Organisms	Mus musculus
Macromolecule	Terminal deoxynucleotidyltransferase short isoform (protein) 5'-D(P(BRU)P(BRU)P(BRU)P(BRU))-3' (nucleic acid)
Unique Ligands	MG, NA

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1KFS \| pdb_00001kfs	Download File View File

DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX

Brautigam, C.A., Steitz, T.A.

(1998) J Mol Biology 277: 363-377

Released	1998-02-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)) (protein) DNA (5'-D(GPCPTPTPAPCP*G)-3') (nucleic acid)
Unique Ligands	MG, ZN

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1KLN \| pdb_00001kln	Download File View File

DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX

Beese, L.S., Derbyshire, V., Steitz, T.A.

(1993) Science 260: 352-355

Released	1994-11-30
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)) (protein) DNA (5'-D(GPCPCPGPCPGPAPGPGPC)-3') (nucleic acid) DNA (5'-D(GPCPCPTPCPGPCPGPGPCPGPGP*C)-3') (nucleic acid)
Unique Ligands	ZN

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1KRP \| pdb_00001krp	Download File View File

DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex

Brautigam, C.A., Steitz, T.A.

(1998) J Mol Biology 277: 363-377

Released	1998-02-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)) (protein) DNA (5'-D(PTPTP*PST)-3') (nucleic acid)
Unique Ligands	ZN

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1KSP \| pdb_00001ksp	Download File View File

DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex

Brautigam, C.A., Steitz, T.A.

(1998) J Mol Biology 277: 363-377

Released	1998-02-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (DNA POLYMERASE I-KLENOW FRAGMENT (E.C.2.7.7.7)) (protein) DNA (5'-D(PTPTP*PST)-3') (nucleic acid)
Unique Ligands	ZN

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1L3S \| pdb_00001l3s	Download File View File

Crystal Structure of Bacillus DNA Polymerase I Fragment complexed to 9 base pairs of duplex DNA.

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 1.7 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA Polymerase I (protein) 5'-D(GPACPGPTPAPCPGPTPGPAPTPCPGPCPA)-3' (nucleic acid) 5'-D(GPCPGPAPTPCPAPCP*G)-3' (nucleic acid)
Unique Ligands	MG, SO4
Unique branched monosaccharides	FRU, GLC

1 to 25 of 1,706 Structures

Page 1 of 69

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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

10MH | pdb_000010mh

1BDX | pdb_00001bdx

1BPX | pdb_00001bpx

1BPY | pdb_00001bpy

1BPZ | pdb_00001bpz

1CEZ | pdb_00001cez

1CLQ | pdb_00001clq

1D0E | pdb_00001d0e

1D8Y | pdb_00001d8y

1DCT | pdb_00001dct

1FJX | pdb_00001fjx

1G38 | pdb_00001g38

1HUO | pdb_00001huo

1HUZ | pdb_00001huz

1I6J | pdb_00001i6j

1IG9 | pdb_00001ig9

1IXY | pdb_00001ixy

1JX4 | pdb_00001jx4

1JXL | pdb_00001jxl

1KDH | pdb_00001kdh

1KFS | pdb_00001kfs

1KLN | pdb_00001kln

1KRP | pdb_00001krp

1KSP | pdb_00001ksp

1L3S | pdb_00001l3s