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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "APE1"

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Search Summary

This query matches 62 Structures.

Refinements

Structure Determination Methodology

experimental (62)

Scientific Name of Source Organism

	Homo sapiens (57)
	synthetic construct (42)
	Saccharomyces cerevisiae S288C (4)
	Saccharomyces cerevisiae (1)

Taxonomy

	Eukaryota (62)
	other sequences (42)

Experimental Method

	X-RAY DIFFRACTION (60)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

	Protein (62)
	DNA (42)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (22)
	2.0 - 2.5 (25)
	2.5 - 3.0 (7)
	3.0 - 3.5 (2)
	> 4.5 (1)

Release Date

	2000 - 2004 (1)
	2010 - 2014 (6)
	2015 - 2019 (28)
	2020 - 2024 (27)

Enzyme Classification Name

	Hydrolases (62)
	Lyases (48)

Symmetry Type

	Asymmetric (57)
	Tetrahedral (4)
	Cyclic (1)

SCOP Classification

	Alpha and beta proteins (a+b) (11)
	Artifacts (4)

AllSelected

1 to 25 of 62 Structures

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1E9N \| pdb_00001e9n	Download File View File

A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism

Beernink, P.T., Segelke, B.W., Rupp, B.

(2001) J Mol Biology 307: 1023

Released	2001-02-16
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (protein)
Unique Ligands	PB

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3U8U \| pdb_00003u8u	Download File View File

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

Agarwal, R., Naidu, M.D.

To be published

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	CL, MG

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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

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4LND \| pdb_00004lnd	Download File View File

Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor

Manvilla, B.A., Pozharski, E., Toth, E.A., Drohat, A.C.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2555-2562

Released	2013-11-27
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	MG

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4QH9 \| pdb_00004qh9	Download File View File

Crystal structure of Mn2+ bound human APE1

Chen, Q., He, H., Georgiadis, M.M.

(2014) Biochemistry 53: 6520-6529

Released	2014-11-12
Method	X-RAY DIFFRACTION 2.175 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	EDO, MN

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4QHD \| pdb_00004qhd	Download File View File

Crystal structure of apo human APE1

He, H., Chen, Q., Georgiadis, M.M.

(2014) Biochemistry 53: 6520-6529

Released	2014-11-12
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	EDO

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4QHE \| pdb_00004qhe	Download File View File

Crystal structure of Mg2+ bound human APE1

He, H., Chen, Q., Georgiadis, M.M.

(2014) Biochemistry 53: 6520-6529

Released	2014-11-12
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	EDO, MG

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4R8F \| pdb_00004r8f	Download File View File

Crystal structure of yeast aminopeptidase 1 (Ape1)

Su, M.-Y., Chang, C.-I.

(2015) Autophagy 11: 1580-1593

Released	2015-08-12
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)

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5CFG \| pdb_00005cfg	Download File View File

C2 crystal form of APE1 with Mg2+

Morera, S., Vigouroux, A.

(2016) Biochimie 128-129: 20-33

Released	2016-07-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein)
Unique Ligands	MG

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5DFF \| pdb_00005dff	Download File View File

Human APE1 product complex

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

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

Released	2015-10-14
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPGPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(P(3DR)PCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid)
Unique Ligands	CL, EDO, MG, PEG

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5DFH \| pdb_00005dfh	Download File View File

Human APE1 mismatch product complex

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

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

Released	2015-10-14
Method	X-RAY DIFFRACTION 1.949 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGPT)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPGPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(P(3DR)PCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid)
Unique Ligands	EDO, MG

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5DFI \| pdb_00005dfi	Download File View File

Human APE1 phosphorothioate substrate complex

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

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

Released	2015-10-14
Method	X-RAY DIFFRACTION 1.63 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

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5DFJ \| pdb_00005dfj	Download File View File

Human APE1 E96Q/D210N mismatch substrate complex

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

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

Released	2015-10-14
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) DNA (5'-D(GPCPTPGPAPTPGPCPGPTP(3DR)PCPGPAPCPGPGPAPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPTPCPCPGPTPCPGPGPGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid)
Unique Ligands	CL, EDO

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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

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5JGF \| pdb_00005jgf	Download File View File

Crystal structure of mApe1

Noda, N.N., Adachi, W., Inagaki, F.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)
Unique Ligands	ZN

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5JH9 \| pdb_00005jh9	Download File View File

Crystal structure of prApe1

Noda, N.N., Adachi, W., Inagaki, F.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)
Unique Ligands	CAC, ZN

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5JHC \| pdb_00005jhc	Download File View File

Crystal structure of the self-assembled propeptides from Ape1

Yamasaki, A., Noda, N.N.

(2016) Cell Rep 16: 19-27

Released	2016-06-29
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar aminopeptidase 1 (protein)

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5JM9 \| pdb_00005jm9	Download File View File

Structure of S. cerevesiae mApe1 dodecamer

Sachse, C., Bertipaglia, C.

(2016) EMBO Rep 17: 1044-1060

Released	2016-06-15
Method	ELECTRON MICROSCOPY 24 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar aminopeptidase 1 (protein)

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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)

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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

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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

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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

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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

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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

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6BOQ \| pdb_00006boq	Download File View File

Human APE1 substrate complex with an A/A mismatch adjacent the THF

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

(2018) Acta Crystallogr D Struct Biol 74: 760-768

Released	2018-08-15
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-(apurinic or apyrimidinic site) lyase (protein) 21-mer DNA (nucleic acid)
Unique Ligands	EDO

1 to 25 of 62 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

1E9N | pdb_00001e9n

3U8U | pdb_00003u8u

4IEM | pdb_00004iem

4LND | pdb_00004lnd

4QH9 | pdb_00004qh9

4QHD | pdb_00004qhd

4QHE | pdb_00004qhe

4R8F | pdb_00004r8f

5CFG | pdb_00005cfg

5DFF | pdb_00005dff

5DFH | pdb_00005dfh

5DFI | pdb_00005dfi

5DFJ | pdb_00005dfj

5DG0 | pdb_00005dg0

5JGF | pdb_00005jgf

5JH9 | pdb_00005jh9

5JHC | pdb_00005jhc

5JM9 | pdb_00005jm9

5WN0 | pdb_00005wn0

5WN1 | pdb_00005wn1

5WN2 | pdb_00005wn2

5WN3 | pdb_00005wn3

5WN4 | pdb_00005wn4

5WN5 | pdb_00005wn5

6BOQ | pdb_00006boq