2F1N
 
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2DDR
 | | 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
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6W2P
 | | 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
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6W3U
 | | 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
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6W3L
 | | 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
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6W0Q
 | | 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
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6W43
 | | 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
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6W4I
 | | 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
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6WCD
 | | 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
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4F1R
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5UVG
 | | 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
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4FVA
 | | 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
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5WN0
 | | 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
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5WN2
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4FPV
 | | 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
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5WN3
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5WN1
 | | 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
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4F1H
 | | 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
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5WN5
 | | 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
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5WN4
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4GZ1
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4GYZ
 | | 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
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4GZ0
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5CFE
 | | 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
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5CFG
 | | 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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