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5UVG
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BU of 5uvg by Molmil
Crystal structure of the human neutral sphingomyelinase 2 (nSMase2) catalytic domain with insertion deleted and calcium bound
Descriptor: CALCIUM ION, Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3
Authors:Airola, M.V, Guja, K.E, Garcia-Diaz, M, Hannun, Y.A.
Deposit date:2017-02-20
Release date:2017-06-28
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (1.849 Å)
Cite:Structure of human nSMase2 reveals an interdomain allosteric activation mechanism for ceramide generation.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
3MPR
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BU of 3mpr by Molmil
Crystal Structure of endonuclease/exonuclease/phosphatase family protein from Bacteroides thetaiotaomicron, Northeast Structural Genomics Consortium Target BtR318A
Descriptor: ACETIC ACID, BROMIDE ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Kuzin, A, Su, M, Seetharaman, J, Mao, M, Xiao, R, Ciccosanti, C, Lee, D, Everett, J.K, Nair, R, Acton, T.B, Rost, B, Montelione, G.T, Hunt, J.F, Tong, L, Northeast Structural Genomics Consortium (NESG)
Deposit date:2010-04-27
Release date:2010-05-26
Last modified:2019-07-17
Method:X-RAY DIFFRACTION (1.899 Å)
Cite:Northeast Structural Genomics Consortium Target BtR318A
To be Published
3NGO
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BU of 3ngo by Molmil
Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA
Descriptor: 5'-D(*AP*AP*AP*A)-3', CCR4-NOT transcription complex subunit 6-like, MAGNESIUM ION
Authors:Wang, H, Morita, M, Yang, W, Bartlam, M, Yamamoto, T, Rao, Z.
Deposit date:2010-06-12
Release date:2010-07-28
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity.
Embo J., 2010
7KIU
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BU of 7kiu by Molmil
Structure of recombinant human DNase1L3 in complex with Mg2+
Descriptor: Deoxyribonuclease gamma, MAGNESIUM ION
Authors:McCord, J.J, Keyel, P.A, Sutton, R.B.
Deposit date:2020-10-24
Release date:2021-12-01
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.22 Å)
Cite:Structural features of Dnase1L3 responsible for serum antigen clearance.
Commun Biol, 5, 2022
3NGQ
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BU of 3ngq by Molmil
Crystal structure of the human CNOT6L nuclease domain
Descriptor: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, CCR4-NOT transcription complex subunit 6-like, MAGNESIUM ION
Authors:Wang, H, Morita, M, Yang, W, Bartlam, M, Yamamoto, T, Rao, Z.
Deposit date:2010-06-13
Release date:2010-07-28
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity.
Embo J., 2010
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
3NGN
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BU of 3ngn by Molmil
Crystal structure of the human CNOT6L nuclease domain in complex with AMP
Descriptor: ADENOSINE MONOPHOSPHATE, CCR4-NOT transcription complex subunit 6-like
Authors:Wang, H, Morita, M, Yang, W, Bartlam, M, Yamamoto, T, Rao, Z.
Deposit date:2010-06-12
Release date:2010-07-28
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity.
Embo J., 2010
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
3U8U
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BU of 3u8u by Molmil
Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form
Descriptor: CHLORIDE ION, DNA-(apurinic or apyrimidinic site) lyase, MAGNESIUM ION
Authors:Agarwal, R, Naidu, M.D.
Deposit date:2011-10-17
Release date:2011-10-26
Last modified:2023-09-13
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form
To be Published
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
3W2X
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BU of 3w2x by Molmil
Crystal structure of DNA uridine endonuclease Mth212
Descriptor: Exodeoxyribonuclease, FORMIC ACID, MAGNESIUM ION
Authors:Tabata, N, Shida, T, Arai, R.
Deposit date:2012-12-06
Release date:2013-12-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal structure of DNA uridine endonuclease Mth212
To be Published
5WN0
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BU of 5wn0 by Molmil
APE1 exonuclease substrate complex with a C/G match
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*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:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2017-07-31
Release date:2018-02-28
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
7LPH
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BU of 7lph by Molmil
APE1 Mn-bound product complex with abasic ribonucleotide DNA
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Freudenthal, B.D, Hoitsma, N.M.
Deposit date:2021-02-11
Release date:2021-08-04
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
7LPJ
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BU of 7lpj by Molmil
APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase, ...
Authors:Freudenthal, B.D, Hoitsma, N.M.
Deposit date:2021-02-11
Release date:2021-08-04
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.56 Å)
Cite:Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
7LPI
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BU of 7lpi by Molmil
APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase
Authors:Freudenthal, B.D, Hoitsma, N.M.
Deposit date:2021-02-11
Release date:2021-08-04
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
7LPG
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BU of 7lpg by Molmil
APE1 product complex with abasic ribonucleotide DNA
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Freudenthal, B.D, Hoitsma, N.M.
Deposit date:2021-02-11
Release date:2021-08-04
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
5WN2
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BU of 5wn2 by Molmil
APE1 exonuclease substrate complex with phosphoglycolate
Descriptor: 1,2-ETHANEDIOL, 2-PHOSPHOGLYCOLIC ACID, CALCIUM ION, ...
Authors:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2017-07-31
Release date:2018-02-28
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (2.288 Å)
Cite:Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
3W2Y
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BU of 3w2y by Molmil
Crystal structure of DNA uridine endonuclease Mth212 mutant W205S
Descriptor: DI(HYDROXYETHYL)ETHER, Exodeoxyribonuclease, FORMIC ACID, ...
Authors:Tabata, N, Shida, T, Arai, R.
Deposit date:2012-12-06
Release date:2013-12-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of DNA uridine endonuclease Mth212
To be Published
9DP4
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BU of 9dp4 by Molmil
APE1 N174Q Product Complex with Abasic DNA
Descriptor: DI(HYDROXYETHYL)ETHER, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
Authors:DeHart, K.D, Hoitsma, N.M, Freudenthal, B.D.
Deposit date:2024-09-20
Release date:2024-10-09
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:N174 Physically and Chemically Stabilizes the APE1 Endonuclease Reaction
To Be Published
9DP2
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BU of 9dp2 by Molmil
APE1 N174A Product Complex with Abasic DNA
Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
Authors:DeHart, K.D, Freudenthal, B.D.
Deposit date:2024-09-20
Release date:2024-10-09
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:N174 Physically and Chemically Stabilizes Abasic DNA During the APE1 Endonuclease Reaction
To Be Published
9DP1
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BU of 9dp1 by Molmil
APE1 N174A Substrate Complex with Abasic DNA
Descriptor: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA repair nuclease/redox regulator APEX1, ...
Authors:DeHart, K.M, Freudenthal, B.D.
Deposit date:2024-09-20
Release date:2024-10-09
Method:X-RAY DIFFRACTION (2.29 Å)
Cite:N174 Physically and Chemically Stabilizes the Endonuclease Reaction of APE1
To Be Published
9DP3
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BU of 9dp3 by Molmil
APE1 N174D Product Complex with Abasic DNA
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ...
Authors:Hoitsma, N.M, DeHart, K.D, Freudenthal, B.D.
Deposit date:2024-09-20
Release date:2024-10-09
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:N174 Physically and Chemically Stabilizes Abasic DNA During the APE1 Endonuclease Reaction
To Be Published
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:2024-10-23
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
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

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