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2F1N
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BU of 2f1n by Molmil
Structure of CdtB, the biologically active subunit of Cytolethal Distending Toxin
Descriptor: Cytolethal distending toxin subunit B
Authors:Hontz, J.S, Yoder, M.D, Dreyfus, L.A.
Deposit date:2005-11-14
Release date:2006-07-04
Last modified:2023-08-23
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Differences in Crystal and Solution Structures of the Cytolethal Distending Toxin B Subunit: RELEVANCE TO NUCLEAR TRANSLOCATION AND FUNCTIONAL ACTIVATION.
J.Biol.Chem., 281, 2006
2DDR
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BU of 2ddr by Molmil
Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion
Descriptor: CALCIUM 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 (1.4 Å)
Cite:Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
J.Biol.Chem., 281, 2006
6W2P
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BU of 6w2p by Molmil
APE1 endonuclease product complex L104R
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*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
Authors:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2020-03-06
Release date:2020-06-10
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6W3U
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BU of 6w3u by Molmil
APE1 exonuclease substrate complex R237C
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, CHLORIDE ION, ...
Authors:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2020-03-09
Release date:2020-06-10
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6W3L
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BU of 6w3l by Molmil
APE1 exonuclease substrate complex wild-type
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, DNA-(apurinic or apyrimidinic site) lyase, ...
Authors:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2020-03-09
Release date:2020-06-10
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.59 Å)
Cite:Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6W0Q
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BU of 6w0q by Molmil
APE1 endonuclease product complex D148E
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ...
Authors:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2020-03-02
Release date:2020-06-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6W43
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BU of 6w43 by Molmil
APE1 AP-endonuclease product complex R237C
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Freudenthal, B.D, Whitaker, A.M.
Deposit date:2020-03-10
Release date:2020-06-10
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Molecular and structural characterization of disease-associated APE1 polymorphisms.
DNA Repair (Amst.), 91-92, 2020
6W4I
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BU of 6w4i by Molmil
APE1 Y269A product complex with abasic DNA
Descriptor: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(P*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
Authors:Freudenthal, B.D, Hoitsma, N.M.
Deposit date:2020-03-10
Release date:2020-06-17
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Nucleic Acids Res., 48, 2020
6WCD
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BU of 6wcd by Molmil
Crystal Structure of Xenopus laevis APE2 Catalytic Domain
Descriptor: 1,2-ETHANEDIOL, 1,4-BUTANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Wojtaszek, J.L, Wallace, B.D, Williams, R.S.
Deposit date:2020-03-30
Release date:2020-05-06
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and Are Reversed by the APE2 Nuclease.
Mol.Cell, 78, 2020
4F1R
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BU of 4f1r by Molmil
Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginos
Descriptor: Catabolite repression control protein
Authors:Zhang, H, Wei, Y, Gao, Z.Q, Dong, Y.H.
Deposit date:2012-05-07
Release date:2013-02-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.201 Å)
Cite:Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginosa.
Iubmb Life, 65, 2013
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
4FVA
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BU of 4fva by Molmil
Crystal structure of truncated Caenorhabditis elegans TDP2
Descriptor: 1,2-ETHANEDIOL, 5'-tyrosyl-DNA phosphodiesterase, MAGNESIUM ION, ...
Authors:Shi, K, Kurahashi, K, Aihara, H.
Deposit date:2012-06-29
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
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
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
4FPV
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BU of 4fpv by Molmil
Crystal structure of D. rerio TDP2 complexed with single strand DNA product
Descriptor: DNA (5'-D(P*TP*GP*CP*AP*G)-3'), GLYCEROL, MAGNESIUM ION, ...
Authors:Shi, K, Kurahashi, K, Aihara, H.
Deposit date:2012-06-22
Release date:2012-10-31
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
5WN3
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BU of 5wn3 by Molmil
APE1 F266A exonuclease substrate complex with a C/T mismatch
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, CHLORIDE 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 Å)
Cite:Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
5WN1
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BU of 5wn1 by Molmil
APE1 exonuclease product complex
Descriptor: CALCIUM ION, CHLORIDE ION, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-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 (2.3 Å)
Cite:Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
4F1H
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BU of 4f1h by Molmil
Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA
Descriptor: DNA (5'-D(P*TP*GP*CP*AP*G)-3'), GLYCEROL, MAGNESIUM ION, ...
Authors:Shi, K, Kurahashi, K, Aihara, H.
Deposit date:2012-05-06
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (1.662 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
5WN5
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BU of 5wn5 by Molmil
APE1 exonuclease substrate complex with a C/T mismatch and Mn2+
Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*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 (2.2 Å)
Cite:Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
5WN4
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BU of 5wn4 by Molmil
APE1 exonuclease substrate complex with a C/T mismatch
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, CHLORIDE 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 (2.1 Å)
Cite:Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9, 2018
4GZ1
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BU of 4gz1 by Molmil
Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3'), FORMIC ACID, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
4GYZ
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BU of 4gyz by Molmil
Mus Musculus Tdp2 Bound to dAMP and Mg2+
Descriptor: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE, CHLORIDE ION, MAGNESIUM ION, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.556 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
4GZ0
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BU of 4gz0 by Molmil
Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex
Descriptor: 1,2-ETHANEDIOL, 6-aminohexan-1-ol, ACETATE ION, ...
Authors:Schellenberg, M.J, Williams, R.S.
Deposit date:2012-09-05
Release date:2012-10-31
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.113 Å)
Cite:Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Nat.Struct.Mol.Biol., 19, 2012
5CFE
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BU of 5cfe by Molmil
Bacillus subtilis AP endonuclease ExoA
Descriptor: CALCIUM ION, DI(HYDROXYETHYL)ETHER, Exodeoxyribonuclease
Authors:Morera, S, Vigouroux, A.
Deposit date:2015-07-08
Release date:2016-07-06
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.
Biochimie, 128-129, 2016
5CFG
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BU of 5cfg by Molmil
C2 crystal form of APE1 with Mg2+
Descriptor: DNA-(apurinic or apyrimidinic site) lyase, MAGNESIUM ION
Authors:Morera, S, Vigouroux, A.
Deposit date:2015-07-08
Release date:2016-07-06
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.
Biochimie, 128-129, 2016

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