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6BOU
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BU of 6bou by Molmil
Human APE1 substrate complex with an T/C mismatch adjacent the THF
分子名称: 21-mer DNA, DNA-(apurinic or apyrimidinic site) lyase
著者Freudenthal, B.D, Whitaker, A.M, Fairlamb, M.S.
登録日2017-11-20
公開日2018-08-15
最終更新日2023-10-04
実験手法X-RAY DIFFRACTION (2.538 Å)
主引用文献Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Acta Crystallogr D Struct Biol, 74, 2018
7NXV
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BU of 7nxv by Molmil
Crystal structure of the complex of DNase I/G-actin/PPP1R15A_582-621
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE-5'-TRIPHOSPHATE, Actin, ...
著者Yan, Y, Ron, D.
登録日2021-03-19
公開日2021-09-29
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.55 Å)
主引用文献Higher-order phosphatase-substrate contacts terminate the integrated stress response.
Nat.Struct.Mol.Biol., 28, 2021
4B5I
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BU of 4b5i by Molmil
Product complex of Neisseria AP endonuclease in presence of metal ions
分子名称: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3', 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP)-3', ...
著者Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S.
登録日2012-08-03
公開日2012-10-17
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (2.555 Å)
主引用文献Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Proc. Natl. Acad. Sci. U.S.A., 109, 2012
4GYZ
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BU of 4gyz by Molmil
Mus Musculus Tdp2 Bound to dAMP and Mg2+
分子名称: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE, CHLORIDE ION, MAGNESIUM ION, ...
著者Schellenberg, M.J, Williams, R.S.
登録日2012-09-05
公開日2012-10-31
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (2.556 Å)
主引用文献Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
7LPJ
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BU of 7lpj by Molmil
APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA
分子名称: 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, ...
著者Freudenthal, B.D, Hoitsma, N.M.
登録日2021-02-11
公開日2021-08-04
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.56 Å)
主引用文献Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
6W3L
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BU of 6w3l by Molmil
APE1 exonuclease substrate complex wild-type
分子名称: 1,2-ETHANEDIOL, CALCIUM ION, DNA-(apurinic or apyrimidinic site) lyase, ...
著者Freudenthal, B.D, Whitaker, A.M.
登録日2020-03-09
公開日2020-06-10
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.59 Å)
主引用文献Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6MAL
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BU of 6mal by Molmil
Structure of human Nocturnin C-terminal domain
分子名称: MAGNESIUM ION, Nocturnin
著者Estrella, M.A, Du, J, Korennykh, A.
登録日2018-08-28
公開日2018-09-05
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal Structure of Human Nocturnin Catalytic Domain.
Sci Rep, 8, 2018
5WN0
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BU of 5wn0 by Molmil
APE1 exonuclease substrate complex with a C/G match
分子名称: 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'), ...
著者Freudenthal, B.D, Whitaker, A.M.
登録日2017-07-31
公開日2018-02-28
最終更新日2023-10-04
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
3G0A
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BU of 3g0a by Molmil
Mth0212 with two bound manganese ions
分子名称: Exodeoxyribonuclease, GLYCEROL, MANGANESE (II) ION, ...
著者Lakomek, K, Dickmanns, A, Ficner, R.
登録日2009-01-27
公開日2010-03-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
J.Mol.Biol., 399, 2010
2A41
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BU of 2a41 by Molmil
Ternary complex of the WH2 Domain of WIP with Actin-DNAse I
分子名称: ADENOSINE-5'-TRIPHOSPHATE, Actin, alpha skeletal muscle, ...
著者Chereau, D, Kerff, F, Dominguez, R.
登録日2005-06-27
公開日2005-11-01
最終更新日2023-08-23
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly
Proc.Natl.Acad.Sci.Usa, 102, 2005
3I46
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BU of 3i46 by Molmil
Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound calcium ions
分子名称: Beta-hemolysin, CALCIUM ION, CHLORIDE ION
著者Huseby, M, Shi, K, Kruse, A.C, Ohlendorf, D.H.
登録日2009-07-01
公開日2010-07-14
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence
To be Published
3G4T
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BU of 3g4t by Molmil
Mth0212 (WT) in complex with a 7bp dsDNA
分子名称: 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3', Exodeoxyribonuclease, ...
著者Lakomek, K, Dickmanns, A, Ficner, R.
登録日2009-02-04
公開日2010-03-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2.64 Å)
主引用文献Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
J.Mol.Biol., 399, 2010
1DEW
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BU of 1dew by Molmil
CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA
分子名称: 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, ...
著者Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A.
登録日1999-11-15
公開日2000-02-02
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.65 Å)
主引用文献DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
Nature, 403, 2000
6W3N
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BU of 6w3n by Molmil
APE1 exonuclease substrate complex D148E
分子名称: 1,2-ETHANEDIOL, CALCIUM ION, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3'), ...
著者Freudenthal, B.D, Whitaker, A.M.
登録日2020-03-09
公開日2020-06-10
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.69 Å)
主引用文献Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6NF0
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BU of 6nf0 by Molmil
Nocturnin with bound NADPH substrate
分子名称: CALCIUM ION, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, Nocturnin
著者Estrella, M.A, Du, J, Korennykh, A.
登録日2018-12-18
公開日2019-05-01
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献The metabolites NADP+and NADPH are the targets of the circadian protein Nocturnin (Curled).
Nat Commun, 10, 2019
7CD5
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BU of 7cd5 by Molmil
mAPE1-blunt-ended dsDNA product complex
分子名称: DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3'), DNA-(apurinic or apyrimidinic site) endonuclease
著者Liu, T.C, Hsiao, Y.Y.
登録日2020-06-18
公開日2021-01-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.
Nat Commun, 12, 2021
7CD6
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BU of 7cd6 by Molmil
mAPE1-recessed dsDNA product complex
分子名称: DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3'), DNA-(apurinic or apyrimidinic site) endonuclease
著者Liu, T.C, Hsiao, Y.Y.
登録日2020-06-18
公開日2021-01-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.701 Å)
主引用文献APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.
Nat Commun, 12, 2021
7N3Y
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BU of 7n3y by Molmil
Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA
分子名称: 1,2-ETHANEDIOL, CALCIUM ION, CITRIC ACID, ...
著者Wojtaszek, J.L, Krahn, J, Wallace, B.D, Williams, R.S.
登録日2021-06-02
公開日2022-09-28
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.73 Å)
主引用文献Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2.
Cell Rep, 41, 2022
4B5G
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BU of 4b5g by Molmil
Substrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 2)
分子名称: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3', EXODEOXYRIBONUCLEASE
著者Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S.
登録日2012-08-03
公開日2012-10-17
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Proc. Natl. Acad. Sci. U.S.A., 109, 2012
4B5M
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BU of 4b5m by Molmil
Neisseria AP endonuclease bound to the substrate with a cytosine orphan base
分子名称: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3', 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP)-3', ...
著者Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S.
登録日2012-08-06
公開日2012-10-17
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (2.758 Å)
主引用文献Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Proc. Natl. Acad. Sci. U.S.A., 109, 2012
2ISI
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BU of 2isi by Molmil
Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand
分子名称: DNA-(apurinic or apyrimidinic site) lyase, MAGNESIUM ION, PHOSPHATE ION
著者Agarwal, R, Naidu, M.D.
登録日2006-10-17
公開日2006-10-31
最終更新日2023-08-30
実験手法X-RAY DIFFRACTION (2.76 Å)
主引用文献Crystal structure of hApe1 in a new crystal form with a bound ligand: implications on catalytic mechanism and its inhibition
To be Published
6W4T
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BU of 6w4t by Molmil
APE1 Y269A phosphorothioate substrate complex with abasic DNA
分子名称: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase
著者Freudenthal, B.D, Hoitsma, N.M.
登録日2020-03-11
公開日2020-06-17
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.77 Å)
主引用文献AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Nucleic Acids Res., 48, 2020
7N8S
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BU of 7n8s by Molmil
LINE-1 endonuclease domain complex with DNA
分子名称: DNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3'), DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)-3'), LINE-1 retrotransposable element ORF2 protein
著者Korolev, S, Miller, I.
登録日2021-06-15
公開日2021-10-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.79 Å)
主引用文献Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
Nucleic Acids Res., 49, 2021
5INN
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BU of 5inn by Molmil
Mouse Tdp2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp conformations
分子名称: CHLORIDE ION, GLYCEROL, SULFATE ION, ...
著者Schellenberg, M.J, Appel, C.D, Williams, R.S.
登録日2016-03-07
公開日2016-04-27
最終更新日2023-09-27
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.
Nucleic Acids Res., 44, 2016
8KA5
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BU of 8ka5 by Molmil
Arabidopsis AP endonuclease ARP complex with 20bp THF-containing DNA
分子名称: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE, DNA (43-MER), DNA-(apurinic or apyrimidinic site) endonuclease, ...
著者Guo, W.T, Wu, B.X.
登録日2023-08-02
公開日2024-02-21
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Structural insights into the catalytic mechanism of the AP endonuclease AtARP.
Structure, 2024

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