PDB: 48855 resultsInfo pagesStatus searchChemie searchBIRD

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3DNB	HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER Descriptor: DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*TP*GP*G)-3'), MAGNESIUM ION Authors: Prive, G.G, Dickerson, R.E. Deposit date: 1988-03-18 Release date: 1989-01-09 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (1.3 Å) Cite: Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J.Mol.Biol., 217, 1991
2IIE	single chain Integration Host Factor protein (scIHF2) in complex with DNA Descriptor: DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), Integration host factor, ... Authors: Bao, Q, Droege, P, Davey, C.A. Deposit date: 2006-09-28 Release date: 2007-02-20 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.41 Å) Cite: A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending J.Mol.Biol., 367, 2007
9BAQ	CryoEM structure of DIM2-HP1-H3K9me3-DNA complex Descriptor: DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3'), DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3'), DNA (cytosine-5-)-methyltransferase, ... Authors: Song, J, Shao, Z. Deposit date: 2024-04-04 Release date: 2024-07-24 Last modified: 2025-02-05 Method: ELECTRON MICROSCOPY (2.79 Å) Cite: Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation. Nat Commun, 15, 2024
2IIF	single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA Descriptor: DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3'), Integration host factor, ... Authors: Bao, Q, Droege, P, Davey, C.A. Deposit date: 2006-09-28 Release date: 2007-02-20 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (2.72 Å) Cite: A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending J.Mol.Biol., 367, 2007
5JVT	Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG Descriptor: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3'), Friend leukemia integration 1 transcription factor, ... Authors: Hou, C, Tsodikov, O.V. Deposit date: 2016-05-11 Release date: 2016-09-14 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1. Nucleic Acids Res., 44, 2016
7N5U	ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 21) Descriptor: DNA Strain II, DNA Strand I, ZINC ION, ... Authors: Horton, J.R, Ren, R, Cheng, X. Deposit date: 2021-06-06 Release date: 2022-06-08 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (2.86 Å) Cite: Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. J.Biol.Chem., 299, 2023
7N5V	ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 20) Descriptor: DNA Strand I, DNA Strand II, ZINC ION, ... Authors: Horton, J.R, Ren, R, Cheng, X. Deposit date: 2021-06-06 Release date: 2022-06-08 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (3.08 Å) Cite: Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. J.Biol.Chem., 299, 2023
5DB6	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dC Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-20 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.83 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
5DB7	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dT Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.209 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
5DBC	Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dG Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*GP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.402 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
2VAN	Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses Descriptor: DNA POLYMERSE BETA Authors: Chan, H, Chou, C, Tang, K, Niebuhr, M, Tung, C, Tsai, M. Deposit date: 2007-09-03 Release date: 2008-04-15 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Mismatched Dntp Incorporation by DNA Polymerase Beta Does not Proceed Via Globally Different Conformational Pathways. Nucleic Acids Res., 36, 2008
5DBA	Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dT Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (1.965 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
5DB8	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*AP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.547 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
5XMA	Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group Descriptor: DNA (36-MER), DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3'), Repair DNA polymerase X Authors: Liu, H.H, Gan, J.H. Deposit date: 2017-05-13 Release date: 2018-01-24 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (3.8 Å) Cite: Crystal structure of an RNA-cleaving DNAzyme. Nat Commun, 8, 2017
5XS0	Structure of a ssDNA bound to the outer DNA binding site of RAD52 Descriptor: DNA repair protein RAD52 homolog, ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3'), ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3'), ... Authors: Saotome, M, Saito, K, Yasuda, T, Sugiyama, S, Kurumizaka, H, Kagawa, W. Deposit date: 2017-06-11 Release date: 2018-04-25 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural Basis of Homology-Directed DNA Repair Mediated by RAD52 iScience, 3, 2018
8AAN	The nucleoprotein complex of Rep protein with iteron containing dsDNA and DUE ssDNA. Descriptor: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*T)-3'), DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3'), DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-3'), ... Authors: Nowacka, M, Wegrzyn, K. Deposit date: 2022-07-01 Release date: 2023-09-27 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.19 Å) Cite: Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation. Nucleic Acids Res., 51, 2023
7RPW	Archaeal DNA ligase and heterotrimeric PCNA in complex with adenylated DNA Descriptor: ADENOSINE MONOPHOSPHATE, DNA ligase, DNA polymerase sliding clamp 1, ... Authors: Sverzhinsky, A, Pascal, J.M. Deposit date: 2021-08-04 Release date: 2021-11-17 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (4.38 Å) Cite: Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure, 30, 2022
7RPO	Archaeal DNA ligase and heterotrimeric PCNA in complex with non-ligatable DNA Descriptor: ADENOSINE MONOPHOSPHATE, DNA ligase, DNA polymerase sliding clamp 1, ... Authors: Sverzhinsky, A, Pascal, J.M. Deposit date: 2021-08-03 Release date: 2021-11-17 Last modified: 2024-11-13 Method: ELECTRON MICROSCOPY (4.16 Å) Cite: Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure, 30, 2022
4UQM	Crystal structure determination of uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans in complex with DNA - new insights into the role of the Leucine-loop for damage recognition and repair Descriptor: 5'-D(*CP*CP*TP*AP*TP*CP*CP*AP*AAB*GP*TP*CP*TP*CP*CP*G)-3', 5'-D(*GP*CP*GP*GP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*AP*G)-3', CHLORIDE ION, ... Authors: Pedersen, H.L, Johnson, K.A, McVey, C.E, Leiros, I, Moe, E. Deposit date: 2014-06-24 Release date: 2015-08-12 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (1.35 Å) Cite: Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA. Acta Crystallogr. D Biol. Crystallogr., 71, 2015
5XXP	Crystal structure of CbnR_DBD-DNA complex Descriptor: DNA (25-MER), LysR-type regulatory protein Authors: Senda, T, Senda, M. Deposit date: 2017-07-04 Release date: 2018-01-17 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.55 Å) Cite: Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region FEBS J., 285, 2018
5XM9	Crystal structure of AsfvPolX in complex with DNA enzyme. Descriptor: DNA (23-mer), DNA (36-MER), Repair DNA polymerase X Authors: Liu, H.H, Gan, J.H. Deposit date: 2017-05-13 Release date: 2018-01-24 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (3.053 Å) Cite: Crystal structure of an RNA-cleaving DNAzyme. Nat Commun, 8, 2017
3DFV	Adjacent GATA DNA binding Descriptor: DNA (5'-D(*DAP*DAP*DGP*DCP*DAP*DGP*DAP*DTP*DAP*DAP*DGP*DTP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DG)-3'), DNA (5'-D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*DTP*DTP*DAP*DTP*DCP*DTP*DGP*DC)-3'), Trans-acting T-cell-specific transcription factor GATA-3, ... Authors: Bates, D.L, Kim, G.K, Guo, L, Chen, L. Deposit date: 2008-06-12 Release date: 2008-07-29 Last modified: 2024-10-30 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA. J.Mol.Biol., 381, 2008
8HX1	Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis Descriptor: Putative starvation-induced DNA protecting protein/Ferritin and Dps Authors: Dutta, S, Garg, P. Deposit date: 2023-01-03 Release date: 2024-07-10 Last modified: 2025-06-18 Method: ELECTRON MICROSCOPY (3.29 Å) Cite: Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegmatis Dps2. J.Mol.Biol., 436, 2024
5D2S	Crystal structure of STPR from Bombyx mori in complex with 18-bp DNA containing four repetitive units of ATAC Descriptor: DNA (36-MER), Fibroin-modulator-binding protein-1 Authors: Cheng, W. Deposit date: 2015-08-06 Release date: 2016-03-23 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structures of an all-alpha protein running along the DNA major groove. Nucleic Acids Res., 2016
5D2Q	Crystal structure of STPR from Bombyx Mori in complex with 20-bp DNA derived from +290 site of the fibroin gene Descriptor: DNA (40-MER), Fibroin-modulator-binding protein-1 Authors: Cheng, W. Deposit date: 2015-08-06 Release date: 2016-03-23 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Structures of an all-alpha protein running along the DNA major groove. Nucleic Acids Res., 2016

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