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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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

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Search Summary

This query matches 172 Structures.

Refinements

Structure Determination Methodology

experimental (172)

Scientific Name of Source Organism

	Homo sapiens (144)
	synthetic construct (68)
	Geobacillus stearothermophilus (10)
	Drosophila melanogaster (8)
	Arabidopsis thaliana (2)
	Clostridium acetobutylicum (2)
	Saccharomyces cerevisiae (2)
	Acanthamoeba polyphaga mimivirus (1)
	Methanocaldococcus jannaschii (1)
	Methanosarcina mazei Go1 (1)

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Taxonomy

	Eukaryota (156)
	other sequences (68)
	Bacteria (13)
	Archaea (2)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (171)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (172)
	DNA (171)
	NA-hybrid (3)

Refinement Resolution (Å)

	1.5 - 2.0 (48)
	2.0 - 2.5 (91)
	2.5 - 3.0 (28)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (10)
	2005 - 2009 (41)
	2010 - 2014 (71)
	2015 - 2019 (37)
	2020 - 2024 (13)

Enzyme Classification Name

	Lyases (164)
	Transferases (101)
	Hydrolases (57)

Symmetry Type

	Asymmetric (169)
	Cyclic (3)

SCOP Classification

	All alpha proteins (77)
	Alpha and beta proteins (a+b) (65)
	Artifacts (12)
	Alpha and beta proteins (a/b) (7)
	All beta proteins (8)
	Small proteins (8)

AllSelected

1 to 25 of 172 Structures

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1DE8 \| pdb_00001de8	Download File View File

HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

Mol, C.D., Izumi, T., Mitra, S., Tainer, J.A.

(2000) Nature 403: 451-456

Released	2000-02-02
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Homo sapiens
Macromolecule	MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE (protein) DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPAPCP(3DR)PGPAPTPCPG)-3') (nucleic acid)

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1DE9 \| pdb_00001de9	Download File View File

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

Mol, C.D., Izumi, T., Mitra, S., Tainer, J.A.

(2000) Nature 403: 451-456

Released	2000-02-02
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE (protein) 5'-d(CPTPAPC)-3' (nucleic acid) 5'-d(GPAPTPCPGPGPTPAPG)-3' (nucleic acid) 5'-d(P(3DR)PGPAPTPC)-3' (nucleic acid)
Unique Ligands	MN

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1DEW \| pdb_00001dew	Download File View File

CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA

Mol, C.D., Izumi, T., Mitra, S., Tainer, J.A.

(2000) Nature 403: 451-456

Released	2000-02-02
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE (protein) 5'-D(GPCPGPTPCPCP(3DR)PCPGPAPCPGPAPCPG)-3' (nucleic acid) 5'-D(GPTPCPGPTPCPGPGPGPGPAPCPGP*C)-3' (nucleic acid)
Unique Ligands	SO4

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1EBM \| pdb_00001ebm	Download File View File

CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE

Bruner, S.D., Norman, D.P., Verdine, G.L.

(2000) Nature 403: 859-866

Released	2000-03-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	8-OXOGUANINE DNA GLYCOSYLASE (protein) DNA (5'-D(GPCPGPTPCPCPAP(8OG)PGPTPCPTPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3') (nucleic acid)
Unique Ligands	CA

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1TEZ \| pdb_00001tez	Download File View File

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

Essen, L.-O., Carell, T., Mees, A., Klar, T.

(2004) Science 306: 1789-1793

Released	2004-12-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Synechococcus elongatus PCC 6301 synthetic construct
Macromolecule	Deoxyribodipyrimidine photo-lyase type I (protein) 5'-D(APTPCPGPGPCPT(TCP)PCPGPC)-3' (nucleic acid) 5'-D(TPCPGPC)-3' (nucleic acid) 5'-D(PCPGPAPAPGPCPCPGPA)-3' (nucleic acid) 5'-D(PGPCPCPGP*A)-3' (nucleic acid)
Unique Ligands	FAD, HDF, MG

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2VTB \| pdb_00002vtb	Download File View File

Structure of cryptochrome 3 - DNA complex

Pokorny, R., Klar, T., Hennecke, U., Carell, T., Batschauer, A., Essen, L.-O.

(2008) Proc Natl Acad Sci U S A 105: 21023

Released	2009-06-02
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Arabidopsis thaliana Homo sapiens
Macromolecule	CRYPTOCHROME DASH (protein) 5'-D(DTDTDTDT*DTP)-3' (nucleic acid)
Unique Ligands	ACT, CL, FAD, MHF

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2WB2 \| pdb_00002wb2	Download File View File

Drosophila Melanogaster (6-4) Photolyase Bound To double stranded Dna containing a T(6-4)C Photolesion

Glas, A.F., Schneider, S., Maul, M.J., Hennecke, U., Carell, T.

(2009) Chemistry 15: 10387

Released	2009-03-17
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Drosophila melanogaster synthetic construct
Macromolecule	PHOTOLYASE (protein) 5'-D(APCPAPGPCPGPGP64PPZPGPCPAP GPGPT)-3' (nucleic acid) 5'-D(TPAPCPCPTPGPCPGPAPCPCPGPCPTPG)-3' (nucleic acid)
Unique Ligands	FAD

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2WQ6 \| pdb_00002wq6	Download File View File

Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(Dewar)C lesion

Glas, A.F., Kaya, E., Schneider, S., Maul, M.J., Carell, T.

(2010) J Am Chem Soc 132: 3254

Released	2010-02-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660P (protein) 5'-D(APCPAPGPCPGPGPTDYPCDWPGP* CPAPAPGPT)-3' (nucleic acid) 5'-D(TPAPCPCPTPGPCPGPAPCP* CPGPCPTPG)-3' (nucleic acid)
Unique Ligands	FAD

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2WQ7 \| pdb_00002wq7	Download File View File

Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(6-4)C lesion

Glas, A.F., Kaya, E., Schneider, S., Maul, M.J., Carell, T.

(2010) J Am Chem Soc 132: 3254

Released	2010-02-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660P (protein) 5'-D(APCPAPGPCPGPGPTDYPZPGP* CPAPAPGPT)-3' (nucleic acid) 5'-D(TPAPCPCPTPGPCPGPAPCP* CPGPCPTPG)-3' (nucleic acid)
Unique Ligands	FAD

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2XHI \| pdb_00002xhi	Download File View File

Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase

Dalhus, B., Forsbring, M., Helle, I.H., Backe, P.H., Forstrom, R.J., Alseth, I., Bjoras, M.

(2011) Structure 19: 117

Released	2011-01-26
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	N-GLYCOSYLASE/DNA LYASE (protein) 5'-D(GPCPGPTPCPCPAP(8OG)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

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2XRZ \| pdb_00002xrz	Download File View File

X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei in complex with intact CPD-lesion

Kiontke, S., Geisselbrecht, Y., Pokorny, R., Carell, T., Batschauer, A., Essen, L.O.

(2011) EMBO J 30: 4437

Released	2011-09-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Methanosarcina mazei Go1 synthetic construct
Macromolecule	DEOXYRIBODIPYRIMIDINE PHOTOLYASE (protein) COUNTERSTRAND-OLIGONUCLEOTIDE (nucleic acid) CPD-COMPRISING OLIGONUCLEOTIDE (nucleic acid)
Unique Ligands	ACT, FAD, GOL, SO4

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3CVU \| pdb_00003cvu	Download File View File

Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion

Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Schlichting, I., Carell, T.

(2008) Angew Chem Int Ed Engl 47: 10076-10080

Released	2008-11-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660p (protein) DNA (5'-D(DAPDCPDAPDGPDCPDGPDGP(64T)P(5PY)PDGPDCPDAPDGPDGPDT)-3') (nucleic acid) DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTPDG)-3') (nucleic acid)
Unique Ligands	FAD

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3CVV \| pdb_00003cvv	Download File View File

Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and F0 cofactor

Glas, A.F., Maul, M.J., Cryle, M.J., Barends, T.R.M., Schneider, S., Kaya, E., Schlichting, I., Carell, T.

(2009) Proc Natl Acad Sci U S A 106: 11540-11545

Released	2009-06-16
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660p (protein) DNA (5'-D(DAPDCPDAPDGPDCPDGPDGP(64T)P(5PY)PDGPDCPDAPDGPDGPDT)-3') (nucleic acid) DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTPDG)-3') (nucleic acid)
Unique Ligands	EDO, FAD, FO1

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3CVW \| pdb_00003cvw	Download File View File

Drosophila melanogaster (6-4) photolyase H365N mutant bound to ds DNA with a T-T (6-4) photolesion and cofactor F0

Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Schlichting, I., Carell, T.

To be published

Released	2009-10-13
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660p (protein) DNA (5'-D(DAPDCPDAPDGPDCPDGPDGP(64T)P(5PY)PDGPDCPDAPDGPDGPDT)-3') (nucleic acid) DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTPDG)-3') (nucleic acid)
Unique Ligands	FAD, FO1

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3CVX \| pdb_00003cvx	Download File View File

Drosophila melanogaster (6-4) photolyase H369M mutant bound to ds DNA with a T-T (6-4) photolesion

Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Schlichting, I., Carell, T.

To be published

Released	2009-10-13
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660p (protein) DNA (5'-D(DAPDCPDAPDGPDCPDGPDGP(64T)P(5PY)PDGPDCPDAPDGPDGPDT)-3') (nucleic acid) DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTPDG)-3') (nucleic acid)
Unique Ligands	FAD

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3CVY \| pdb_00003cvy	Download File View File

Drosophila melanogaster (6-4) photolyase bound to repaired ds DNA

Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Schlichting, I., Carell, T.

(2008) Angew Chem Int Ed Engl 47: 10076-10080

Released	2008-11-04
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Drosophila melanogaster
Macromolecule	RE11660p (protein) DNA (5'-D(DAPDCPDAPDGPDCPDGPDGPDTPDTPDGPDCPDAPDGPDGPDT)-3') (nucleic acid) DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTPDG)-3') (nucleic acid)
Unique Ligands	FAD

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3GO8 \| pdb_00003go8	Download File View File

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-loop deletion complex

Spong, M.C., Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-12-15
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Geobacillus stearothermophilus synthetic construct
Macromolecule	Formamidopyrimidine-DNA glycosylase (protein) 5'-D(GPCPGPTPCPCP(8OG)PGPAPTPCPTPAPC)-3' (nucleic acid) 5'-D(PGPGPTPAPGPAPTPCPCPGPGPAPCPG)-3' (nucleic acid)
Unique Ligands	ZN

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3GPP \| pdb_00003gpp	Download File View File

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-T224P complex

Spong, M.C., Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(PCPGPTPCPCP(8OG)PGPAPTPCPTPAPC)-3') (nucleic acid) DNA (5'-D(PGPGPTPAPGPAPTPCPCPGPGPAPC)-3') (nucleic acid)
Unique Ligands	ZN

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3GPU \| pdb_00003gpu	Download File View File

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex

Banerjee, A., Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(APGPGPTPAPGPAPCPTPCPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGPCPGPTPCPCP(8OG)PAPGPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	ZN

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3GPX \| pdb_00003gpx	Download File View File

Sequence-matched MutM Interrogation Complex 4 (IC4)

Spong, M.C., Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(AGPGPTPAPGPAPCPTPCPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGPCPGPTPCPCPGPAPGPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	ZN

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3GPY \| pdb_00003gpy	Download File View File

Sequence-matched MutM Lesion Recognition Complex 3 (LRC3)

Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(APGPGPTPAPGPAPTPCPCPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TGPCPGPTPCPCP(8OG)PGPAPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	ZN

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3GQ3 \| pdb_00003gq3	Download File View File

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC5-loop deletion complex

Banerjee, A., Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(APGPGPTPAPGPAPCPCPCPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGPCPGPTPCPCPGP(8OG)PGPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	ZN

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3GQ4 \| pdb_00003gq4	Download File View File

Sequence-matched MutM Lesion Recognition Complex 5 (LRC5)

Spong, M.C., Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(APGPGPTPAPGPAPCPCPCPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGPCPGPTPCPCPGP(8OG)PGPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	GOL, ZN

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3GQ5 \| pdb_00003gq5	Download File View File

Sequence-matched MutM Interrogation Complex 5 (IC5)

Qi, Y., Verdine, G.L.

(2009) Nature 462: 762-766

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(AGPGPTPAPGPAPCPCPCPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGPCPGPTCPCPGPGPGPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	GOL, ZN

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3JR4 \| pdb_00003jr4	Download File View File

MutM interrogating an extrahelical G

Qi, Y., Spong, M.C., Verdine, G.L.

(2010) J Biological Chem 285: 1468-1478

Released	2009-11-03
Method	X-RAY DIFFRACTION 2.601 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA glycosylase (protein) DNA (5'-D(APGPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3') (nucleic acid) DNA (5'-D(TPGCPGPTPCPCPAP(GX1)PGPTPCPTPAPCPC)-3') (nucleic acid)
Unique Ligands	ZN

1 to 25 of 172 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

1DE8 | pdb_00001de8

1DE9 | pdb_00001de9

1DEW | pdb_00001dew

1EBM | pdb_00001ebm

1TEZ | pdb_00001tez

2VTB | pdb_00002vtb

2WB2 | pdb_00002wb2

2WQ6 | pdb_00002wq6

2WQ7 | pdb_00002wq7

2XHI | pdb_00002xhi

2XRZ | pdb_00002xrz

3CVU | pdb_00003cvu

3CVV | pdb_00003cvv

3CVW | pdb_00003cvw

3CVX | pdb_00003cvx

3CVY | pdb_00003cvy

3GO8 | pdb_00003go8

3GPP | pdb_00003gpp

3GPU | pdb_00003gpu

3GPX | pdb_00003gpx

3GPY | pdb_00003gpy

3GQ3 | pdb_00003gq3

3GQ4 | pdb_00003gq4

3GQ5 | pdb_00003gq5

3JR4 | pdb_00003jr4