RCSB PDB: Search

1N39 \| pdb_00001n39	Download File View File

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Norman, D.P., Chung, S.J., Verdine, G.L.

(2003) Biochemistry 42: 1564-1572

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) DNA complement strand (nucleic acid) DNA inhibitor strand (nucleic acid)
Unique Ligands	CA

Explore in 3D

1N3A \| pdb_00001n3a	Download File View File

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Norman, D.P., Chung, S.J., Verdine, G.L.

(2003) Biochemistry 42: 1564-1572

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) DNA complement strand (nucleic acid) DNA inhibitor strand (nucleic acid)
Unique Ligands	CA

Explore in 3D

1N3C \| pdb_00001n3c	Download File View File

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Norman, D.P., Chung, S.J., Verdine, G.L.

(2003) Biochemistry 42: 1564-1572

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 8-oxoG-containing DNA (nucleic acid) DNA complement strand (nucleic acid)
Unique Ligands	CA

Explore in 3D

2I5W \| pdb_00002i5w	Download File View File

Structure of hOGG1 crosslinked to DNA sampling a normal G adjacent to an oxoG

Banerjee, A., Verdine, G.L.

(2006) Proc Natl Acad Sci U S A 103: 15020-15025

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPGPTPAPGPAPCPCPTPGPGPA)-3' (nucleic acid) 5'-D(PCPCPAPGP(G42)PTPCPTPAPC)-3' (nucleic acid)
Unique Ligands	CA, GOL

Explore in 3D

2NOB \| pdb_00002nob	Download File View File

Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(TGPGPTPAPGPAPCPCPTPGPGPAPCPGP*C)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

2NOE \| pdb_00002noe	Download File View File

Structure of catalytically inactive G42A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

2NOF \| pdb_00002nof	Download File View File

Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPCPGPTPCCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

2NOH \| pdb_00002noh	Download File View File

Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

2NOI \| pdb_00002noi	Download File View File

Structure of G42A human 8-oxoguanine glycosylase crosslinked to undamaged G-containing DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPCPGPTPCCPAPGPGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

2NOL \| pdb_00002nol	Download File View File

Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxoG DNA

Banerjee, A., Radom, C.T., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.57 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

2NOZ \| pdb_00002noz	Download File View File

Structure of Q315F human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J Biological Chem 282: 9182-9194

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GCPGPTPCPCPAP(G42)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGTPAPGPAPCPCPTPGPGPAPCPGPC)-3' (nucleic acid)
Unique Ligands	CA

Explore in 3D

3I0W \| pdb_00003i0w	Download File View File

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG

Faucher, F., Doublie, S.

(2009) DNA Repair (Amst) 8: 1283-1289

Released	2009-09-29
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Clostridium acetobutylicum
Macromolecule	8-oxoguanine-DNA-glycosylase (protein) 5'-D(APTPCPCPAP(8OG)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPCPTPGPGP*A)-3' (nucleic acid)
Unique Ligands	EDO, NA

Explore in 3D

3I0X \| pdb_00003i0x	Download File View File

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing adenine opposite to 8-oxoG

Faucher, F., Doublie, S.

(2009) DNA Repair (Amst) 8: 1283-1289

Released	2009-09-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Clostridium acetobutylicum
Macromolecule	8-oxoguanine-DNA-glycosylase (protein) 5'-D(APTPCPCPAP(8OG)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPAPCPAPTPGPGP*A)-3' (nucleic acid)
Unique Ligands	NA

Explore in 3D

3IH7 \| pdb_00003ih7	Download File View File

Crystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA

Verdine, G.L., Crenshaw, C.M., Oo, K.S., Kutchukian, P.S.

To be published

Released	2010-11-03
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(GPGPTPAPGPAPCPCPTPGPGPAPCPG)-3' (nucleic acid) 5'-D(APTPCPTPGPGPAPCPCPTPGPCPA)-3' (nucleic acid)

Explore in 3D

3KNT \| pdb_00003knt	Download File View File

Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine

Faucher, F., Doublie, S.

(2010) J Mol Biology 397: 46-56

Released	2010-02-02
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	N-glycosylase/DNA lyase (protein) 5'-D(APCPGPTPCPCPAP(8OG)PGPTPCPTPAPCPC)-3' (nucleic acid) 5'-D(TPGPGPTPAPGPAPCPCPTPGPGPAPCPG)-3' (nucleic acid)
Unique Ligands	NA

Explore in 3D

3KTU \| pdb_00003ktu	Download File View File

Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA

Verdine, G.L., Lee, S.M.

To be published

Released	2010-07-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	N-glycosylase/DNA lyase (protein) DNA (5'-D(GPGPTPAPGPAPCPCPTPGPGPAPC)-3') (nucleic acid) DNA (5'-D(GPTPCPCPAP(FDG)PGPTPCPTPAP*C)-3') (nucleic acid)
Unique Ligands	CA

Explore in 3D

4IEM \| pdb_00004iem	Download File View File

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

Tsutakawa, S.E., Mol, C.D., Arvai, A.S., Tainer, J.A.

(2013) J Biological Chem 288: 8445-8455

Released	2013-01-23
Method	X-RAY DIFFRACTION 2.3936 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPAPC)-3') (nucleic acid) DNA (5'-D(P(3DR)PGPAPTPCPG)-3') (nucleic acid)
Unique Ligands	MG, NA

Explore in 3D

4NRW \| pdb_00004nrw	Download File View File

MvNei1-G86D

Prakash, A., Doublie, S.

(2014) DNA Repair (Amst) 14: 17-26

Released	2014-01-01
Method	X-RAY DIFFRACTION 2.845 Å
Organisms	Acanthamoeba polyphaga mimivirus
Macromolecule	formamidopyrimidine-DNA glycosylase (protein) 5'-D(CPGPTPCPCPAP(3DR)PGPTPCPTPAPC)-3' (nucleic acid) 5'-D(GPTPAPGPAPCPCPTPGPGPAPCPG)-3' (nucleic acid)

Explore in 3D

5DG0 \| pdb_00005dg0	Download File View File

Human APE1 phosphorothioate substrate complex with Mn2+

Freudenthal, B.D., Wilson, S.H.

(2015) Nat Struct Mol Biol 22: 924-931

Released	2015-10-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGP(OMC)P(48Z)PCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPGPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid)
Unique Ligands	CL, EDO, MN

Explore in 3D

5WN0 \| pdb_00005wn0	Download File View File

APE1 exonuclease substrate complex with a C/G match

Freudenthal, B.D., Whitaker, A.M.

(2018) Nat Commun 9: 399-399

Released	2018-02-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPAPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PTPCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid)

Explore in 3D

5WN1 \| pdb_00005wn1	Download File View File

APE1 exonuclease product complex

Freudenthal, B.D., Whitaker, A.M.

(2018) Nat Commun 9: 399-399

Released	2018-02-28
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPG)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPAPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PTPCPGPAPCPGPGPAPTPCP*C)-3') (nucleic acid)
Unique Ligands	CA, CL, NA

Explore in 3D

5WN2 \| pdb_00005wn2	Download File View File

APE1 exonuclease substrate complex with phosphoglycolate

Freudenthal, B.D., Whitaker, A.M.

(2018) Nat Commun 9: 399-399

Released	2018-02-28
Method	X-RAY DIFFRACTION 2.288 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPG)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPAPCPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PTPCPGPAPCPGPGPAPTPCP*C)-3') (nucleic acid)
Unique Ligands	CA, EDO, NA, PGA

Explore in 3D

5WN3 \| pdb_00005wn3	Download File View File

APE1 F266A exonuclease substrate complex with a C/T mismatch

Freudenthal, B.D., Whitaker, A.M.

(2018) Nat Commun 9: 399-399

Released	2018-02-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGP(DV3))-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPAPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PTPCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid)
Unique Ligands	CA, CL, EDO, NA

Explore in 3D

5WN4 \| pdb_00005wn4	Download File View File

APE1 exonuclease substrate complex with a C/T mismatch

Freudenthal, B.D., Whitaker, A.M.

(2018) Nat Commun 9: 399-399

Released	2018-02-28
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGP(DV3))-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPAPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PTPCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid)
Unique Ligands	CA, CL, EDO, NA

Explore in 3D

5WN5 \| pdb_00005wn5	Download File View File

APE1 exonuclease substrate complex with a C/T mismatch and Mn2+

Freudenthal, B.D., Whitaker, A.M.

(2018) Nat Commun 9: 399-399

Released	2018-02-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGP(DV3))-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPAPTPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(PTPCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid)
Unique Ligands	EDO, MN, NA

Prepare Data

Validate Data

Deposit Data

Help and Resources

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

1N39 | pdb_00001n39

1N3A | pdb_00001n3a

1N3C | pdb_00001n3c

2I5W | pdb_00002i5w

2NOB | pdb_00002nob

2NOE | pdb_00002noe

2NOF | pdb_00002nof

2NOH | pdb_00002noh

2NOI | pdb_00002noi

2NOL | pdb_00002nol

2NOZ | pdb_00002noz

3I0W | pdb_00003i0w

3I0X | pdb_00003i0x

3IH7 | pdb_00003ih7

3KNT | pdb_00003knt

3KTU | pdb_00003ktu

4IEM | pdb_00004iem

4NRW | pdb_00004nrw

5DG0 | pdb_00005dg0

5WN0 | pdb_00005wn0

5WN1 | pdb_00005wn1

5WN2 | pdb_00005wn2

5WN3 | pdb_00005wn3

5WN4 | pdb_00005wn4

5WN5 | pdb_00005wn5