PDB: 45817 resultsInfo pagesStatus searchChemie searchBIRD

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4DA4	Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA Descriptor: CITRIC ACID, DNA (cytosine-5)-methyltransferase 1, DNA_LOWER_STRAND, ... Authors: Song, J, Patel, D.J. Deposit date: 2012-01-12 Release date: 2012-02-22 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation. Science, 335, 2012
5TD5	Crystal Structure of Human APOBEC3B variant complexed with ssDNA Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(P*TP*TP*CP*AP*T)-3'), ... Authors: Shi, K, Banerjee, S, Kurahashi, K, Aihara, H. Deposit date: 2016-09-16 Release date: 2016-12-28 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (1.718 Å) Cite: Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol., 24, 2017
1HUT	THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER Descriptor: ALPHA-Thrombin heavy chain, ALPHA-Thrombin light chain, D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide, ... Authors: Padmanabhan, K, Padmanabhan, K.P, Ferrara, J.D, Sadler, J.E, Tulinsky, A. Deposit date: 1993-05-27 Release date: 1994-06-22 Last modified: 2013-02-27 Method: X-RAY DIFFRACTION (2.9 Å) Cite: The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. J.Biol.Chem., 268, 1993
5CLB	Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer A) Descriptor: AlkD, DNA (5'-D(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3') Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.766 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
5CL3	Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (100% substrate at 4 hours) Descriptor: AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3') Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.971 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
5CL8	Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 144 hours) Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3'), ... Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.38 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
5CLE	Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic-site analog and a free 3-methyladenine nucleobase Descriptor: 3-METHYL-3H-PURIN-6-YLAMINE, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(3DR)P*AP*GP*TP*CP*CP*G)-3'), ... Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.73 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
5CL9	Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 240 hours) Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3'), ... Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.538 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
5CLD	Alkylpurine DNA glycosylase AlkD bound to DNA containing an oxocarbenium-intermediate analog and a free 3-methyladenine nucleobase Descriptor: 3-METHYL-3H-PURIN-6-YLAMINE, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3'), ... Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.541 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
5CLA	Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 360 hours) Descriptor: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine, AlkD, DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3'), ... Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.541 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
8SV3	7-Deazapurines and 5-Halogenpyrimidine DNA duplex Descriptor: GLYCEROL, MAGNESIUM ION, Modified DNA, ... Authors: Pallan, P.S, Egli, M. Deposit date: 2023-05-15 Release date: 2023-10-04 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.51 Å) Cite: Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry, 62, 2023
8SV4	7-Deazapurines and 5-Halogenpyrimidine DNA duplex Descriptor: 1,2-ETHANEDIOL, 2-[2-(2-ethoxyethoxy)ethoxy]ethanol, ACETATE ION, ... Authors: Pallan, P.S, Egli, M. Deposit date: 2023-05-15 Release date: 2023-10-04 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry, 62, 2023
4DL4	Human DNA polymerase eta inserting dCMPNPP opposite the 3'G of cisplatin crosslinked Gs (Pt-GG1). Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, Cisplatin, DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*G)-3'), ... Authors: Zhao, Y, Biertumpfel, C, Gregory, M, Hua, Y.-J, Hanaoka, F, Yang, W. Deposit date: 2012-02-05 Release date: 2012-05-09 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2 Å) Cite: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Proc.Natl.Acad.Sci.USA, 109, 2012
5CLC	Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer B) Descriptor: AlkD, DNA (5'-D(*AP*AP*GP*CP*CP*(DZM)P*CP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*GP*TP*GP*GP*CP*T)-3') Authors: Mullins, E.A, Eichman, B.F. Deposit date: 2015-07-16 Release date: 2015-10-28 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.729 Å) Cite: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527, 2015
4DL3	Human DNA polymerase eta inserting dCMPNPP opposite GG template (GG0b). Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(*TP*AP*CP*GP*GP*TP*CP*AP*CP*AP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*C)-3'), ... Authors: Zhao, Y, Biertumpfel, C, Gregory, M, Hua, Y, Hanaoka, F, Yang, W. Deposit date: 2012-02-05 Release date: 2012-05-09 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Proc.Natl.Acad.Sci.USA, 109, 2012
4DL5	Human DNA polymerase eta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2). Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, Cisplatin, DNA (5'-D(*TP*AP*CP*GP*GP*TP*CP*AP*CP*AP*CP*T)-3'), ... Authors: Zhao, Y, Biertumpfel, C, Gregory, M, Hanaoka, F, Hua, Y, Yang, W. Deposit date: 2012-02-05 Release date: 2012-05-09 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.92 Å) Cite: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Proc.Natl.Acad.Sci.USA, 109, 2012
1DC1	RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD Descriptor: 1,4-DIETHYLENE DIOXIDE, BSOBI RESTRICTION ENDONUCLEASE, DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3') Authors: van der Woerd, M.J, Pelletier, J.J, Xu, S.-Y, Friedman, A.M. Deposit date: 1999-11-04 Release date: 2001-02-21 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure, 9, 2001
1D54	ANTHRACYCLINE BINDING TO DNA: HIGH RESOLUTION STRUCTURE OF D(TGTACA) COMPLEXED WITH 4'-EPIADRIAMYCIN Descriptor: 4'-EPIDOXORUBICIN, DNA (5'-D(*TP*GP*TP*AP*CP*A)-3') Authors: Leonard, G.A, Brown, T, Hunter, W.N. Deposit date: 1992-01-06 Release date: 1993-04-15 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.4 Å) Cite: Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin. Eur.J.Biochem., 204, 1992
8BI4	Helical shell of CCMV capsid protein on DNA origami 6HB-2k Descriptor: Coat protein Authors: Kumpula, E.-P, Seitz, I, Kostiainen, M.A, Huiskonen, J.T. Deposit date: 2022-11-01 Release date: 2023-07-05 Last modified: 2023-10-25 Method: ELECTRON MICROSCOPY (4.3 Å) Cite: DNA-origami-directed virus capsid polymorphism. Nat Nanotechnol, 18, 2023
3M4A	Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site Descriptor: ACETIC ACID, DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3'), ... Authors: Patel, A, Yakovleva, L, Shuman, S, Mondragon, A. Deposit date: 2010-03-10 Release date: 2010-07-14 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.65 Å) Cite: Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site. Structure, 18, 2010
2HPM	Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III Descriptor: CHLORIDE ION, DNA Polymerase III alpha subunit, MAGNESIUM ION, ... Authors: Bailey, S, Wing, R.A, Steitz, T.A. Deposit date: 2006-07-17 Release date: 2006-09-19 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (3.7 Å) Cite: The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases. Cell(Cambridge,Mass.), 126, 2006
6G0A	The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution. Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*DC)-3'), ... Authors: Parkash, V, Johansson, E. Deposit date: 2018-03-16 Release date: 2019-01-30 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (2.62 Å) Cite: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon. Nat Commun, 10, 2019
6FWK	The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3'), ... Authors: Parkash, V, Johansson, E. Deposit date: 2018-03-06 Release date: 2019-01-30 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.503 Å) Cite: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon. Nat Commun, 10, 2019
4CIS	Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA Descriptor: (R,R)-2,3-BUTANEDIOL, DNA, FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE, ... Authors: Schneider, S, Sadeghian, K, Flaig, D, Blank, I.D, Strasser, R, Stathis, D, Winnacker, M, Carell, T, Ochsenfeld, C. Deposit date: 2013-12-15 Release date: 2014-06-04 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Ribose-protonated DNA base excision repair: a combined theoretical and experimental study. Angew. Chem. Int. Ed. Engl., 53, 2014
3ZDB	Structure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, di-magnesium and potassium Descriptor: 5OV4 DNA, 5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*CP)-3', ACETATE ION, ... Authors: Hemsworth, G.R, Anstey-Gilbert, C.S, Flemming, C.S, Hodskinson, M.R.G, Zhang, J, Sedelnikova, S.E, Stillman, T.J, Sayers, J.R, Artymiuk, P.J. Deposit date: 2012-11-26 Release date: 2013-07-10 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (1.47 Å) Cite: The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases Nucleic Acids Res., 41, 2013

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