PDB: 45953 resultsInfo pagesStatus searchChemie searchBIRD

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1IYR	NMR Structure Ensemble Of Dff-C Domain Descriptor: DNA FRAGMENTATION FACTOR ALPHA SUBUNIT Authors: Fukushima, K, Kikuchi, J, Koshiba, S, Kigawa, T, Kuroda, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2002-09-05 Release date: 2002-09-25 Last modified: 2023-12-27 Method: SOLUTION NMR Cite: Solution Structure of the Dff-C Domain of Dff45/Icad. A Structural Basis for the Regulation of Apoptotic DNA Fragmentation J.Mol.Biol., 321, 2002
2EBW	Solution structure of the BRCT domain from human DNA repair protein REV1 Descriptor: DNA repair protein REV1 Authors: Nagashima, T, Hayashi, F, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2007-02-09 Release date: 2007-08-14 Last modified: 2024-05-29 Method: SOLUTION NMR Cite: Solution structure of the BRCT domain from human DNA repair protein REV1 To be Published
1YFL	T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and Specific Contact and Flipped Base Descriptor: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3', DNA adenine methylase, SINEFUNGIN Authors: Horton, J.R, Liebert, K, Hattman, S, Jeltsch, A, Cheng, X. Deposit date: 2005-01-03 Release date: 2005-05-17 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (3.09 Å) Cite: Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase. Cell(Cambridge,Mass.), 121, 2005
4IOU	Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F Descriptor: DNA dC->dU-editing enzyme APOBEC-3F, ZINC ION Authors: Bohn, M, Shandilya, S.M.D, Schiffer, C.A. Deposit date: 2013-01-08 Release date: 2013-05-29 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.751 Å) Cite: Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain. Structure, 21, 2013
3QKT	Rad50 ABC-ATPase with adjacent coiled-coil region in complex with AMP-PNP Descriptor: DNA double-strand break repair rad50 ATPase, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Authors: Williams, G.J, Williams, R.S, Arvai, A, Moncalian, G, Tainer, J.A. Deposit date: 2011-02-01 Release date: 2011-03-30 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.9 Å) Cite: ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat.Struct.Mol.Biol., 18, 2011
2NBQ	NMR Structure of the C-Terminal Domain of human APOBEC3B Descriptor: DNA dC->dU-editing enzyme APOBEC-3B, ZINC ION Authors: Byeon, I.L, Byeon, C, Gronenborn, A.M. Deposit date: 2016-03-09 Release date: 2016-06-01 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity. Biochemistry, 55, 2016
1YF3	T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact Descriptor: 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3', 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3', DNA adenine methylase, ... Authors: Horton, J.R, Liebert, K, Hattman, S, Jeltsch, A, Cheng, X. Deposit date: 2004-12-30 Release date: 2005-05-17 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (2.29 Å) Cite: Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase. Cell(Cambridge,Mass.), 121, 2005
1YFJ	T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact Descriptor: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3', CALCIUM ION, CHLORIDE ION, ... Authors: Horton, J.R, Liebert, K, Hattman, S, Jeltsch, A, Cheng, X. Deposit date: 2005-01-02 Release date: 2005-05-17 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (2.69 Å) Cite: Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase. Cell(Cambridge,Mass.), 121, 2005
2A1J	Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Descriptor: DNA excision repair protein ERCC-1, DNA repair endonuclease XPF, MERCURY (II) ION Authors: Tsodikov, O.V, Enzlin, J.H, Scharer, O.D, Ellenberger, T. Deposit date: 2005-06-20 Release date: 2005-08-02 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1. Proc.Natl.Acad.Sci.Usa, 102, 2005
2A1I	Crystal Structure of the Central Domain of Human ERCC1 Descriptor: DNA excision repair protein ERCC-1, MERCURY (II) ION Authors: Tsodikov, O.V, Enzlin, J.H, Scharer, O.D, Ellenberger, T. Deposit date: 2005-06-20 Release date: 2005-08-02 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1. Proc.Natl.Acad.Sci.Usa, 102, 2005
6ESF	Nucleosome : Class 1 Descriptor: DNA (147-MER), Histone H2A, Histone H2B 1.1, ... Authors: Bilokapic, S, Halic, M. Deposit date: 2017-10-20 Release date: 2017-12-20 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Histone octamer rearranges to adapt to DNA unwrapping. Nat. Struct. Mol. Biol., 25, 2018
6ESG	Nucleosome breathing : Class 2 Descriptor: DNA (141-MER), Histone H2A, Histone H2B 1.1, ... Authors: Bilokapic, S, Halic, M. Deposit date: 2017-10-20 Release date: 2017-12-20 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (5.4 Å) Cite: Histone octamer rearranges to adapt to DNA unwrapping. Nat. Struct. Mol. Biol., 25, 2018
6ESH	Nucleosome breathing : Class 3 Descriptor: DNA (137-MER), Histone H2A, Histone H2B 1.1, ... Authors: Bilokapic, S, Halic, M. Deposit date: 2017-10-20 Release date: 2017-12-20 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (5.1 Å) Cite: Histone octamer rearranges to adapt to DNA unwrapping. Nat. Struct. Mol. Biol., 25, 2018
6ESI	Nucleosome breathing : Class 4 Descriptor: DNA (133-MER), Histone H2A, Histone H2B 1.1, ... Authors: Bilokapic, S, Halic, M. Deposit date: 2017-10-20 Release date: 2017-12-20 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (6.3 Å) Cite: Histone octamer rearranges to adapt to DNA unwrapping. Nat. Struct. Mol. Biol., 25, 2018
7URK	Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification Descriptor: DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3'), DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3'), DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3'), ... Authors: Sha, R, Vecchioni, S. Deposit date: 2022-04-22 Release date: 2023-04-26 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (3.12 Å) Cite: Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification To Be Published
8DXV	[T:Au+:T--(pH11-pH7; 5s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 5s Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3'), DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3'), ... Authors: Lu, B, Vecchioni, S, Seeman, N.C, Sha, R, Ohayon, Y.P. Deposit date: 2022-08-03 Release date: 2023-08-09 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (4.59 Å) Cite: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs To Be Published
8DXX	[T:Au+:T--(pH11-pH7; 45s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 45s Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3'), DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3'), ... Authors: Lu, B, Vecchioni, S, Seeman, N.C, Sha, R, Ohayon, Y.P. Deposit date: 2022-08-03 Release date: 2023-08-09 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (4.07 Å) Cite: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs To Be Published
8DXY	[T:Au+:T--(pH11-pH7; 180s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 180s Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3'), DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3'), ... Authors: Lu, B, Vecchioni, S, Seeman, N.C, Sha, R, Ohayon, Y.P. Deposit date: 2022-08-03 Release date: 2023-08-09 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (4.87 Å) Cite: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs To Be Published
8DXW	[T:Au+:T--(pH11-pH7; 15s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 15s Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3'), DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3'), ... Authors: Lu, B, Vecchioni, S, Seeman, N.C, Sha, R, Ohayon, Y.P. Deposit date: 2022-08-03 Release date: 2023-08-09 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (4.52 Å) Cite: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs To Be Published
8DXZ	[T:Au+:T--(pH11-pH7; 420s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 420s Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3'), DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3'), ... Authors: Lu, B, Vecchioni, S, Seeman, N.C, Sha, R, Ohayon, Y.P. Deposit date: 2022-08-03 Release date: 2023-08-09 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (4.71 Å) Cite: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs To Be Published
4ZVI	GYRASE B IN COMPLEX WITH 4,5-DIBROMOPYRROLAMIDE-BASED INHIBITOR Descriptor: DNA gyrase subunit B, IODIDE ION, N-(4-{[(4,5-dibromo-1H-pyrrol-2-yl)carbonyl]amino}benzoyl)glycine Authors: Zidar, N, Macut, H, Tomasic, T, Brvar, M, Montalvao, S, Tammela, P, Solmajer, T, Peterlin Masic, L, Ilas, J, Kikelj, D. Deposit date: 2015-05-18 Release date: 2015-07-15 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.2 Å) Cite: N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation. J.Med.Chem., 58, 2015
8CRZ	Crystal structure of alien DNA CTSZZPBSBSZPPBAG in a tetragonal lattice Descriptor: DNA (5'-D(*CP*TP*(JSP)P*(1W5)P*(1W5)P*(1WA)P*(IGU)P*(JSP))-3'), DNA (5'-D(P*(IGU)P*(JSP)P*(1W5)P*(1WA)P*(1WA)P*(IGU)P*AP*G)-3') Authors: Georgiadis, M.M. Deposit date: 2022-05-12 Release date: 2023-05-17 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (1.2 Å) Cite: Alien DNA visualized at high resolution in A- and B-forms To Be Published
6DY9	Crystal structure of double-stranded DNA GGGATCCC; crystals grown in Zn2+ Descriptor: DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*C)-3'), ZINC ION Authors: Hou, C, Tsodikov, O.V. Deposit date: 2018-07-01 Release date: 2019-01-23 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Utilizing guanine coordinated Zn2+ to determine DNA crystal structures by single-wavelength anomalous diffraction Acta Crystallogr.,Sect.D, 75, 2019
5DA7	monomeric PCNA bound to a small protein inhibitor Descriptor: DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen, SULFATE ION, ... Authors: Ladner, J.E, Altieri, A.S, Kelman, Z. Deposit date: 2015-08-19 Release date: 2016-05-11 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.802 Å) Cite: A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Nucleic Acids Res., 44, 2016
1WEW	Solution structure of PHD domain in DNA-binding family protein AAM98074 Descriptor: DNA-binding family protein, ZINC ION Authors: He, F, Muto, Y, Inoue, M, Kigawa, T, Shirouzu, M, Terada, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2004-05-25 Release date: 2004-11-25 Last modified: 2024-05-29 Method: SOLUTION NMR Cite: Solution structure of PHD domain in DNA-binding family protein AAM98074 To be Published

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