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2JC4
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BU of 2jc4 by Molmil
3'-5' exonuclease (NExo) from Neisseria Meningitidis
Descriptor: ACETATE ION, DIHYDROGENPHOSPHATE ION, EXODEOXYRIBONUCLEASE III, ...
Authors:Carpenter, E.P, Corbett, A, Thomson, H, Adacha, J, Jensen, K, Bergeron, J, Kasampalidis, I, Exley, R, Winterbotham, M, Tang, C, Baldwin, G, Freemont, P.
Deposit date:2006-12-19
Release date:2007-03-06
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Ap Endonuclease Paralogues with Distinct Activities in DNA Repair and Bacterial Pathogenesis.
Embo J., 26, 2007
1ZWX
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BU of 1zwx by Molmil
Crystal Structure of SmcL
Descriptor: GLYCEROL, PHOSPHATE ION, sphingomyelinase-c
Authors:Openshaw, A.E.A, Race, P.R, Monzo, H.J, Vasquez-Boland, J.A, Banfield, M.J.
Deposit date:2005-06-06
Release date:2005-08-16
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria.
J.Biol.Chem., 280, 2005
6MKK
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BU of 6mkk by Molmil
Crystallographic solvent mapping analysis of DMSO/Mg bound to APE1
Descriptor: 1,2-ETHANEDIOL, DIMETHYL SULFOXIDE, DNA-(apurinic or apyrimidinic site) lyase, ...
Authors:Georgiadis, M.M, He, H, Chen, Q.
Deposit date:2018-09-25
Release date:2019-01-30
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.442 Å)
Cite:Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
J. Med. Chem., 62, 2019
8SP5
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BU of 8sp5 by Molmil
LINE-1 retrotransposon endonuclease domain complex with Mn2+
Descriptor: LINE-1 retrotransposon endonuclease, MANGANESE (II) ION, SULFATE ION
Authors:D'Ordine, A.M, Jogl, G, Sedivy, J.M.
Deposit date:2023-05-02
Release date:2024-05-22
Method:X-RAY DIFFRACTION (2.23 Å)
Cite:Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease.
Nat Commun, 15, 2024
8SP7
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BU of 8sp7 by Molmil
LINE-1 retrotransposon endonuclease domain complex with tranexamic acid
Descriptor: LINE-1 retrotransposon endonuclease, SULFATE ION, TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID
Authors:D'Ordine, A.M, Jogl, G, Sedivy, J.M.
Deposit date:2023-05-02
Release date:2024-05-22
Method:X-RAY DIFFRACTION (1.83 Å)
Cite:Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease.
Nat Commun, 15, 2024
6NF0
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BU of 6nf0 by Molmil
Nocturnin with bound NADPH substrate
Descriptor: CALCIUM ION, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, Nocturnin
Authors:Estrella, M.A, Du, J, Korennykh, A.
Deposit date:2018-12-18
Release date:2019-05-01
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:The metabolites NADP+and NADPH are the targets of the circadian protein Nocturnin (Curled).
Nat Commun, 10, 2019
6LPM
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BU of 6lpm by Molmil
Crystal structure of AP endonuclease from Deinococcus radioduran
Descriptor: Exodeoxyribonuclease III
Authors:Zhao, Y, He, Y.
Deposit date:2020-01-11
Release date:2020-05-27
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans .
Front Microbiol, 11, 2020
6MAL
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BU of 6mal by Molmil
Structure of human Nocturnin C-terminal domain
Descriptor: MAGNESIUM ION, Nocturnin
Authors:Estrella, M.A, Du, J, Korennykh, A.
Deposit date:2018-08-28
Release date:2018-09-05
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal Structure of Human Nocturnin Catalytic Domain.
Sci Rep, 8, 2018
6MKM
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BU of 6mkm by Molmil
Crystallographic solvent mapping analysis of DMSO/Tris bound to APE1
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, DIMETHYL SULFOXIDE, ...
Authors:Georgiadis, M.M, He, H, Chen, Q.
Deposit date:2018-09-25
Release date:2019-01-30
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.673 Å)
Cite:Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
J. Med. Chem., 62, 2019
6MK3
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BU of 6mk3 by Molmil
Crystallographic solvent mapping analysis of DMSO bound to APE1
Descriptor: 1,2-ETHANEDIOL, DIMETHYL SULFOXIDE, DNA-(apurinic or apyrimidinic site) lyase
Authors:Georgiadis, M.M, He, H, Chen, Q.
Deposit date:2018-09-24
Release date:2019-01-30
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.478 Å)
Cite:Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
J. Med. Chem., 62, 2019
6MKO
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BU of 6mko by Molmil
Crystallographic solvent mapping analysis of glycerol bound to APE1
Descriptor: DNA-(apurinic or apyrimidinic site) lyase, GLYCEROL
Authors:Georgiadis, M.M, He, H, Chen, Q.
Deposit date:2018-09-25
Release date:2019-01-30
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
J. Med. Chem., 62, 2019
1DE9
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BU of 1de9 by Molmil
HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION
Descriptor: 5'-d(*CP*TP*AP*C)-3', 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3', 5'-d(P*(3DR)P*GP*AP*TP*C)-3', ...
Authors:Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A.
Deposit date:1999-11-13
Release date:2000-02-02
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (3 Å)
Cite:DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
Nature, 403, 2000
1DEW
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BU of 1dew by Molmil
CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA
Descriptor: 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3', 5'-D(*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3', MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE, ...
Authors:Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A.
Deposit date:1999-11-15
Release date:2000-02-02
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
Nature, 403, 2000
1DE8
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BU of 1de8 by Molmil
HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA
Descriptor: DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)-3'), MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
Authors:Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A.
Deposit date:1999-11-13
Release date:2000-02-02
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected
Nature, 403, 2000
7SUV
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BU of 7suv by Molmil
APE1 exonuclease substrate complex with 8oxoG opposite A
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Whitaker, A.W, Freudenthal, B.D.
Deposit date:2021-11-18
Release date:2022-09-07
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Processing oxidatively damaged bases at DNA strand breaks by APE1.
Nucleic Acids Res., 50, 2022
7SVB
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BU of 7svb by Molmil
APE1 exonuclease substrate complex with 8oxoG opposite C
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Whitaker, A.W, Freudenthal, B.D.
Deposit date:2021-11-18
Release date:2022-09-07
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.24 Å)
Cite:Processing oxidatively damaged bases at DNA strand breaks by APE1.
Nucleic Acids Res., 50, 2022
7TC3
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BU of 7tc3 by Molmil
Human APE1 in the apo form
Descriptor: 1,2-ETHANEDIOL, DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial
Authors:Pidugu, L.S, Pozharski, E, Drohat, A.C.
Deposit date:2021-12-22
Release date:2022-12-21
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.252 Å)
Cite:Characterizing inhibitors of human AP endonuclease 1.
Plos One, 18, 2023
7TC2
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BU of 7tc2 by Molmil
Human APE1 in complex with 5-nitroindole-2-carboxylic acid
Descriptor: 1,2-ETHANEDIOL, 5-nitro-1H-indole-2-carboxylic acid, DI(HYDROXYETHYL)ETHER, ...
Authors:Pidugu, L.S, Pozharski, E, Drohat, A.C.
Deposit date:2021-12-22
Release date:2022-12-21
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.43 Å)
Cite:Characterizing inhibitors of human AP endonuclease 1.
Plos One, 18, 2023
1DNK
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BU of 1dnk by Molmil
THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3'), DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'), ...
Authors:Weston, S.A, Lahm, A, Suck, D.
Deposit date:1992-08-10
Release date:1994-01-31
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.
J.Mol.Biol., 226, 1992
7TR7
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BU of 7tr7 by Molmil
APE1 product complex with abasic ssDNA
Descriptor: DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase, MAGNESIUM ION
Authors:Freudenthal, B.D, Hoitsma, N.M.
Deposit date:2022-01-28
Release date:2023-04-12
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics.
Nucleic Acids Res., 51, 2023
1HD7
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BU of 1hd7 by Molmil
A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism
Descriptor: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, LEAD (II) ION
Authors:Beernink, P.T, Segelke, B.W, Rupp, B.
Deposit date:2000-11-09
Release date:2001-02-16
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
J.Mol.Biol., 307, 2001
1E9N
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BU of 1e9n by Molmil
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
Descriptor: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, LEAD (II) ION
Authors:Beernink, P.T, Segelke, B.W, Rupp, B.
Deposit date:2000-10-24
Release date:2001-02-16
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
J.Mol.Biol., 307, 2001
2DNJ
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BU of 2dnj by Molmil
DNASE I-INDUCED DNA CONFORMATION. 2 ANGSTROMS STRUCTURE OF A DNASE I-OCTAMER COMPLEX
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 5'-D(*GP*CP*GP*AP*TP*C)-3', 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3', ...
Authors:Lahm, A, Suck, D.
Deposit date:1986-10-21
Release date:1994-01-31
Last modified:2020-10-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex
J.Mol.Biol., 222, 1991
2DDT
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BU of 2ddt by Molmil
Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, MAGNESIUM ION, SULFATE ION, ...
Authors:Ago, H, Oda, M, Tsuge, H, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2006-02-02
Release date:2006-05-02
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
J.Biol.Chem., 281, 2006
2DDS
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BU of 2dds by Molmil
Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion
Descriptor: COBALT (II) ION, Sphingomyelin phosphodiesterase
Authors:Ago, H, Oda, M, Takahashi, M, Tsuge, H, Ochi, S, Katunuma, N, Miyano, M, Sakurai, J, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2006-02-02
Release date:2006-05-02
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
J.Biol.Chem., 281, 2006

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