PDB: 45953 resultsInfo pagesStatus searchChemie searchBIRD

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2W3O	Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Descriptor: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE, CALCIUM ION, DNA REPAIR PROTEIN XRCC1 Authors: Oliver, A.W, Ali, A.A.E, Pearl, L.H. Deposit date: 2008-11-13 Release date: 2009-02-03 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (1.85 Å) Cite: Specific Recognition of a Multiply Phosphorylated Motif in the DNA Repair Scaffold Xrcc1 by the Fha Domain of Human Pnk. Nucleic Acids Res., 37, 2009
4WSZ	Crystal structure of the DNA binding domains of wild type LiaR from E. faecalis Descriptor: ACETATE ION, GLYCEROL, PRASEODYMIUM ION, ... Authors: Davlieva, M, Shamoo, Y. Deposit date: 2014-10-29 Release date: 2015-05-06 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.769 Å) Cite: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
4WT0	Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis Descriptor: PRASEODYMIUM ION, Response regulator receiver domain protein Authors: Davlieva, M, Shamoo, Y. Deposit date: 2014-10-29 Release date: 2015-05-06 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.8 Å) Cite: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
7P2W	E.coli GyrB24 with inhibitor LMD92 (EBL2682) Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-4-[(3-carboxyphenyl)methoxy]-1,3-benzothiazole-6-carboxylic acid, DNA gyrase subunit B, ... Authors: Stevenson, C.E.M, Lawson, D.M, Maxwell, A.M, Henderson, S.R, Kikelj, D, Durcik, M, Zega, A, Zidar, N, Ilas, J, Tomasic, T, Masic, L.P. Deposit date: 2021-07-06 Release date: 2022-07-20 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.65 Å) Cite: Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa. J.Med.Chem., 66, 2023
7P2M	E.coli GyrB24 with inhibitor LMD43 (EBL2560) Descriptor: 2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-phenylmethoxy-1,3-benzothiazole-6-carboxylic acid, DNA gyrase subunit B, PHOSPHATE ION Authors: Stevenson, C.E.M, Lawson, D.M, Maxwell, A.M, Henderson, S.R, Kikelj, D, Durcik, M, Zega, A, Zidar, N, Ilas, J, Tomasic, T, Masic, L.P. Deposit date: 2021-07-06 Release date: 2022-07-20 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.16 Å) Cite: Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa. J.Med.Chem., 66, 2023
4D2I	Crystal structure of the HerA hexameric DNA translocase from Sulfolobus solfataricus bound to AMP-PNP Descriptor: HERA, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Authors: Rzechorzek, N.J, Blackwood, J.K, Bray, S.M, Maman, J.D, Pellegrini, L, Robinson, N.P. Deposit date: 2014-05-09 Release date: 2014-12-03 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.841 Å) Cite: Structure of the Hexameric Hera ATPase Reveals a Mechanism of Translocation-Coupled DNA-End Processing in Archaea Nat.Commun., 5, 2014
404D	CRYSTAL STRUCTURE OF THE RNA/DNA HYBRID R(GAAGAGAAGC). D(GCTTCTCTTC) Descriptor: 5'-D(*GP*CP*TP*TP*CP*TP*CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3' Authors: Conn, G, Brown, T, Leonard, G.A. Deposit date: 1998-06-12 Release date: 1998-12-14 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.5 Å) Cite: The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) shows significant differences to that found in solution. Nucleic Acids Res., 27, 1999
1XPP	Crystal Structure of TA1416,DNA-directed RNA polymerase subunit L, from Thermoplasma acidophilum Descriptor: ACETIC ACID, DNA-directed RNA polymerase subunit L, FORMIC ACID, ... Authors: Kim, Y, Joachimiak, A, Evdokimova, E, Savchenko, A, Edwards, A, Midwest Center for Structural Genomics (MCSG) Deposit date: 2004-10-09 Release date: 2004-11-23 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.6 Å) Cite: Crystal structure of TA1416, DNA-directed RNA polymerase subunit L, from Thermoplasma acidophilum To be Published
1SKM	HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site Descriptor: 5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3', 5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3', Modification methylase HhaI, ... Authors: Horton, J.R, Ratner, G, Banavali, N, Huang, N, Marquez, V.E, MacKerell, A.D, Cheng, X. Deposit date: 2004-03-05 Release date: 2004-08-24 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase Nucleic Acids Res., 32, 2004
1S1K	INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION Descriptor: 5'-D(*CP*CP*(1AP)P*GP*TP*AP*CP*TP*GP*G)-3', CALCIUM ION, SODIUM ION Authors: Hays, F.A, Watson, J, Ho, P.S. Deposit date: 2004-01-06 Release date: 2004-08-31 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Influence of minor groove substituents on the structure of DNA holliday junctions. Biochemistry, 43, 2004
4EW0	mouse MBD4 glycosylase domain in complex with a G:5hmU (5-hydroxymethyluracil) mismatch Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*CP*CP*AP*TP*GP*(5HU)P*GP*CP*TP*GP*A)-3'), DNA (5'-D(*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'), ... Authors: Hashimoto, H, Zhang, X, Cheng, X. Deposit date: 2012-04-26 Release date: 2012-07-11 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.39 Å) Cite: Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Nucleic Acids Res., 40, 2012
3RZJ	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage Descriptor: 2-OXOGLUTARIC ACID, 5'-D(*CP*TP*GP*TP*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3', ... Authors: Yi, C, Chen, B, Qi, B, Zhang, W, Jia, G, Zhang, L, Li, C, Dinner, A, Yang, C, He, C. Deposit date: 2011-05-11 Release date: 2012-06-06 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Duplex interrogation by a direct DNA repair protein in search of base damage Nat.Struct.Mol.Biol., 19, 2012
3RZH	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage Descriptor: 5'-D(*CP*TP*GP*TP*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3', Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, ... Authors: Yi, C, Chen, B, Qi, B, Zhang, W, Jia, G, Zhang, L, Li, C, Dinner, A, Yang, C, He, C. Deposit date: 2011-05-11 Release date: 2012-06-06 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.25 Å) Cite: Duplex interrogation by a direct DNA repair protein in search of base damage Nat.Struct.Mol.Biol., 19, 2012
3RZG	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage Descriptor: 5'-D(*CP*TP*GP*TP*CP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*TP*GP*AP*CP*A)-3', Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, ... Authors: Yi, C, Chen, B, Qi, B, Zhang, W, Jia, G, Zhang, L, Li, C, Dinner, A, Yang, C, He, C. Deposit date: 2011-05-11 Release date: 2012-06-06 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (1.62 Å) Cite: Duplex interrogation by a direct DNA repair protein in search of base damage Nat.Struct.Mol.Biol., 19, 2012
3RZM	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage Descriptor: 5'-D(*AP*TP*GP*TP*AP*TP*AP*AP*CP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*TP*AP*CP*A)-3', Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, ... Authors: Yi, C, Chen, B, Qi, B, Zhang, W, Jia, G, Zhang, L, Li, C, Dinner, A, Yang, C, He, C. Deposit date: 2011-05-11 Release date: 2012-06-06 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (3.06 Å) Cite: Duplex interrogation by a direct DNA repair protein in search of base damage Nat.Struct.Mol.Biol., 19, 2012
3RZK	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage Descriptor: 2-OXOGLUTARIC ACID, 5'-D(*CP*TP*GP*TP*CP*TP*(EDA)P*AP*CP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*GP*AP*CP*A)-3', ... Authors: Yi, C, Chen, B, Qi, B, Zhang, W, Jia, G, Zhang, L, Li, C, Dinner, A, Yang, C, He, C. Deposit date: 2011-05-11 Release date: 2012-06-06 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.78 Å) Cite: Duplex interrogation by a direct DNA repair protein in search of base damage Nat.Struct.Mol.Biol., 19, 2012
8G1I	SpCas9 with sgRNA and target DNA Descriptor: CRISPR-associated endonuclease Cas9/Csn1, DNA E2_NTS, DNA E2_TS, ... Authors: Korolev, S, Gagnon, K. Deposit date: 2023-02-02 Release date: 2023-05-17 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (3.12 Å) Cite: SpCas9 with sgRNA and target DNA To Be Published
3RZL	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage Descriptor: 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3', Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, ... Authors: Yi, C, Chen, B, Qi, B, Zhang, W, Jia, G, Zhang, L, Li, C, Dinner, A, Yang, C, He, C. Deposit date: 2011-05-11 Release date: 2012-06-06 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Duplex interrogation by a direct DNA repair protein in search of base damage Nat.Struct.Mol.Biol., 19, 2012
6PZV	Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Descriptor: CITRATE ANION, DNA (cytosine-5)-methyltransferase 1, Histone H3.3, ... Authors: Ren, W, Song, J. Deposit date: 2019-08-01 Release date: 2020-07-15 Last modified: 2020-08-12 Method: X-RAY DIFFRACTION (3.01 Å) Cite: Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation. Proc.Natl.Acad.Sci.USA, 117, 2020
2W36	Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair Descriptor: 5'-D(*CP*GP*AP*TP*CP*TP*GP*TP*AP*GP*CP)-3', 5'-D(*GP*CP*BRUP*AP*CP*IP*GP*AP*BRUP*CP*GP)-3', ENDONUCLEASE V Authors: Dalhus, B, Arvai, A.S, Rosnes, I, Olsen, O.E, Backe, P.H, Alseth, I, Gao, H, Cao, W, Tainer, J.A, Bjoras, M. Deposit date: 2008-11-06 Release date: 2009-01-20 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structures of Endonuclease V with DNA Reveal Initiation of Deaminated Adenine Repair. Nat.Struct.Mol.Biol., 16, 2009
1N14	Structure and Dynamics of Thioguanine-modified Duplex DNA in Comparison with Unmodified DNA; Structure of Unmodified Duplex DNA Descriptor: 5'-D(*GP*CP*TP*AP*AP*GP*GP*AP*AP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*AP*GP*C)-3' Authors: Somerville, L, Krynetski, E.Y, Krynetskaia, N.F, Beger, R.D, Zhang, W, Marhefka, C.A, Evans, W.E, Kriwacki, R.W. Deposit date: 2002-10-16 Release date: 2002-10-23 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Structure and dynamics of thioguanine-modified duplex DNA J.Biol.Chem., 278, 2003
1RVE	THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS Descriptor: ENDONUCLEASE EcoR V Authors: Winkler, F.K. Deposit date: 1992-02-24 Release date: 1994-01-31 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.5 Å) Cite: The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J., 12, 1993
1R68	Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of MAR70/d(CGATCG) complex Descriptor: 4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN, 5'-D(*CP*GP*AP*TP*CP*G)-3' Authors: Temperini, C, Cirilli, M, Aschi, M, Ughetto, G. Deposit date: 2003-10-15 Release date: 2005-02-22 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.2 Å) Cite: Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of the complex MAR70/d(CGATCG). BIOORG.MED.CHEM., 13, 2005
2W35	Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair Descriptor: 5'-D(*AP*GP*CP*CP*GP*TP)-3', 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3', Endonuclease V, ... Authors: Dalhus, B, Arvai, A.S, Rosnes, I, Olsen, O.E, Backe, P.H, Alseth, I, Gao, H, Cao, W, Tainer, J.A, Bjoras, M. Deposit date: 2008-11-06 Release date: 2009-01-20 Last modified: 2024-06-19 Method: X-RAY DIFFRACTION (2.15 Å) Cite: Structures of Endonuclease V with DNA Reveal Initiation of Deaminated Adenine Repair. Nat.Struct.Mol.Biol., 16, 2009
452D	ACRIDINE BINDING TO DNA Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE, DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') Authors: Thorpe, J.H, Todd, A.K, Cardin, C.J. Deposit date: 1999-02-18 Release date: 2003-03-04 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.6 Å) Cite: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethlyamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution J.Med.Chem., 42, 1999

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