2DDT
| 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
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2DNJ
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2DDS
| 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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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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2F1N
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4B5I
| Product complex of Neisseria AP endonuclease in presence of metal ions | Descriptor: | 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', ... | Authors: | Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S. | Deposit date: | 2012-08-03 | Release date: | 2012-10-17 | Last modified: | 2018-02-28 | Method: | X-RAY DIFFRACTION (2.555 Å) | Cite: | Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc. Natl. Acad. Sci. U.S.A., 109, 2012
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4B5F
| Substrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 1) | Descriptor: | 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3', PUTATIVE EXODEOXYRIBONUCLEASE | Authors: | Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S. | Deposit date: | 2012-08-03 | Release date: | 2012-10-17 | Last modified: | 2018-02-28 | Method: | X-RAY DIFFRACTION (2.005 Å) | Cite: | Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc. Natl. Acad. Sci. U.S.A., 109, 2012
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4B5G
| Substrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 2) | Descriptor: | 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 | Authors: | Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S. | Deposit date: | 2012-08-03 | Release date: | 2012-10-17 | Last modified: | 2018-02-28 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc. Natl. Acad. Sci. U.S.A., 109, 2012
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4B5J
| Neisseria AP endonuclease bound to the substrate with an orphan Adenine base | Descriptor: | 5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3', PUTATIVE EXODEOXYRIBONUCLEASE | Authors: | Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S. | Deposit date: | 2012-08-03 | Release date: | 2012-10-17 | Last modified: | 2018-02-28 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc. Natl. Acad. Sci. U.S.A., 109, 2012
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4AWN
| Structure of recombinant human DNase I (rhDNaseI) in complex with Magnesium and Phosphate. | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Parsiegla, G, Noguere, C, Santell, L, Lazarus, R.A, Bourne, Y. | Deposit date: | 2012-06-04 | Release date: | 2013-01-09 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | The Structure of Human DNase I Bound to Magnesium and Phosphate Ions Points to a Catalytic Mechanism Common to Members of the DNase I-Like Superfamily. Biochemistry, 51, 2012
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4B5H
| Substate bound inactive mutant of Neisseria AP endonuclease in presence of metal ions | Descriptor: | 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*TP*AP*CP*3DRP*CP*AP*TP*CP*GP)-3', MANGANESE (II) ION, ... | Authors: | Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S. | Deposit date: | 2012-08-03 | Release date: | 2012-10-17 | Last modified: | 2018-02-28 | Method: | X-RAY DIFFRACTION (3.05 Å) | Cite: | Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc. Natl. Acad. Sci. U.S.A., 109, 2012
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4B5M
| Neisseria AP endonuclease bound to the substrate with a cytosine orphan base | Descriptor: | 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', ... | Authors: | Lu, D, Silhan, J, MacDonald, J.T, Carpenter, E.P, Jensen, K, Tang, C.M, Baldwin, G.S, Freemont, P.S. | Deposit date: | 2012-08-06 | Release date: | 2012-10-17 | Last modified: | 2018-02-28 | Method: | X-RAY DIFFRACTION (2.758 Å) | Cite: | Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc. Natl. Acad. Sci. U.S.A., 109, 2012
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7LPH
| 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
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7LPJ
| 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
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7LPG
| 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
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7LPI
| 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
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7MCR
| Human Apex/Ref1 homodimer formed under oxidative condition | Descriptor: | DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial, MAGNESIUM ION | Authors: | Nam, Y.W, Yang, S. | Deposit date: | 2021-04-02 | Release date: | 2022-04-06 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | The Development of Novel Apurinic/Aprymidinic Endonuclease/Redox-factor 1 Inhibitors for the Treatment of Human Melanoma To Be Published
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7MEV
| Human Apex/Ref1 monomer with C138A mutation | Descriptor: | DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial, GLYCEROL, ... | Authors: | Nam, Y.W, Yang, S. | Deposit date: | 2021-04-07 | Release date: | 2022-04-13 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | The Development of Novel Apurinic/Aprymidinic Endonuclease/Redox-factor 1 Inhibitors for the Treatment of Human Melanoma To Be Published
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4C1R
| Bacteroides thetaiotaomicron VPI-5482 mannosyl-6-phosphatase Bt3783 | Descriptor: | 1,2-ETHANEDIOL, MAGNESIUM ION, MANNOSYL-6-PHOSPHATASE | Authors: | Cuskin, F, Lowe, E.C, Zhu, Y, Temple, M, Thompson, A.J, Cartmell, A, Piens, K, Bracke, D, Vervecken, W, Munoz-Munoz, J.L, Suits, M.D.L, Boraston, A.B, Williams, S.J, Davies, G.J, Abbott, W.D, Martens, E.C, Gilbert, H.J. | Deposit date: | 2013-08-13 | Release date: | 2013-11-13 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism. Nature, 517, 2015
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7N3Z
| Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, DNA-(apurinic or apyrimidinic site) endonuclease 2, ... | Authors: | Wojtaszek, J.L, Wallace, B.D, Williams, R.S. | Deposit date: | 2021-06-02 | Release date: | 2022-09-28 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Cell Rep, 41, 2022
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7N3Y
| Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, CITRIC ACID, ... | Authors: | Wojtaszek, J.L, Krahn, J, Wallace, B.D, Williams, R.S. | Deposit date: | 2021-06-02 | Release date: | 2022-09-28 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.73 Å) | Cite: | Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Cell Rep, 41, 2022
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7N8K
| LINE-1 endonuclease domain complex with Mg | Descriptor: | ACETATE ION, LINE-1 retrotransposable element ORF2 protein, MAGNESIUM ION, ... | Authors: | Korolev, S, Miller, I. | Deposit date: | 2021-06-15 | Release date: | 2021-10-13 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.01 Å) | Cite: | Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res., 49, 2021
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7N94
| LINE-1 endonuclease domain complex with DNA | Descriptor: | DNA (5'-D(*AP*GP*CP*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*GP*CP*TP*A)-3'), LINE-1 retrotransposable element ORF2 protein | Authors: | Korolev, S, Miller, I. | Deposit date: | 2021-06-16 | Release date: | 2021-10-13 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res., 49, 2021
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7N8S
| LINE-1 endonuclease domain complex with DNA | Descriptor: | 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 | Authors: | Korolev, S, Miller, I. | Deposit date: | 2021-06-15 | Release date: | 2021-10-13 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.79 Å) | Cite: | Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res., 49, 2021
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4F1R
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