PDB: 48855 resultsInfo pagesStatus searchChemie searchBIRD

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6DBO	Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Descriptor: CALCIUM ION, Forward strand of substrate RSS DNA, Recombination activating gene 1 - MBP chimera, ... Authors: Wu, H, Liao, M, Ru, H, Mi, W. Deposit date: 2018-05-03 Release date: 2018-08-01 Last modified: 2024-03-13 Method: ELECTRON MICROSCOPY (4.4 Å) Cite: DNA melting initiates the RAG catalytic pathway. Nat. Struct. Mol. Biol., 25, 2018
6EN1	Structure of the Tn1549 transposon Integrase (aa 82-397, R225K) in complex with a circular intermediate DNA (CI6a-DNA) Descriptor: DI(HYDROXYETHYL)ETHER, DNA (45-MER), Int protein Authors: Rubio-Cosials, A, Barabas, O. Deposit date: 2017-10-04 Release date: 2018-04-04 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (2.67 Å) Cite: Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell, 173, 2018
1DCV	B-DNA DECAMER WITH CENTRAL TA DINUCLEOTIDE Descriptor: DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3') Authors: Eichman, B.F, Vargason, J.M, Mooers, B.H.M, Ho, P.S. Deposit date: 1999-11-05 Release date: 2000-04-17 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.5 Å) Cite: The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proc.Natl.Acad.Sci.USA, 97, 2000
1DIZ	CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA Descriptor: 3-METHYLADENINE DNA GLYCOSYLASE II, DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3'), DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3'), ... Authors: Hollis, T, Ichikawa, Y, Ellenberger, T.E. Deposit date: 1999-11-30 Release date: 2000-03-20 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.5 Å) Cite: DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J., 19, 2000
2E0G	DnaA N-terminal domain Descriptor: Chromosomal replication initiator protein dnaA Authors: Abe, Y, Katayama, T, Ueda, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2006-10-07 Release date: 2007-05-01 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Structure and Function of DnaA N-Terminal Domains: Specific Sites and Mechanisms in Inter-DnaA Interaction and in DnaB Helicase Loading on oriC To be Published
7YGO	DNA duplex containing 5OHU-Hg(II)-T base pairs Descriptor: DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3'), MERCURY (II) ION Authors: Kondo, J, Torigoe, H, Arakawa, F. Deposit date: 2022-07-12 Release date: 2023-05-24 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (2.403 Å) Cite: Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
1BWG	DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES Descriptor: DNA (5'-D(*CP*TP*CP*TP*CP*T)-3'), DNA (5'-D(*GP*AP*CP*TP*GP*AP*GP*AP*GP*AP*CP*GP*TP*A)-3'), DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3') Authors: Asensio, J.L, Brown, T, Lane, A.N. Deposit date: 1998-09-22 Release date: 1999-03-23 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions. Structure Fold.Des., 7, 1999
2RRR	DNA oligomer containing ethylene cross-linked cyclic 2'-deoxyuridylate dimer Descriptor: DNA (5'-D(*CP*CP*TP*TP*CP*AP*TP*TP*AP*CP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*GP*TP*AP*AP*TP*GP*AP*AP*GP*G)-3') Authors: Furuita, K, Murata, S, Jee, J.G, Ichikawa, S, Matsuda, A, Kojima, C. Deposit date: 2011-03-24 Release date: 2011-06-08 Last modified: 2024-05-01 Method: SOLUTION NMR Cite: Structural Feature of Bent DNA Recognized by HMGB1 J.Am.Chem.Soc., 133, 2011
2RRQ	DNA oligomer containing propylene cross-linked cyclic 2'-deoxyuridylate dimer Descriptor: DNA (5'-D(*CP*CP*TP*TP*CP*AP*(JDT)P*TP*AP*CP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*GP*TP*AP*AP*TP*GP*AP*AP*GP*G)-3') Authors: Furuita, K, Murata, S, Jee, J.G, Ichikawa, S, Matsuda, A, Kojima, C. Deposit date: 2011-03-24 Release date: 2011-06-08 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Structural Feature of Bent DNA Recognized by HMGB1 J.Am.Chem.Soc., 133, 2011
6MC3	Crystal structure of a tetrameric DNA fold-back quadruplex Descriptor: DNA (5'-D(*CP*GP*TP*GP*AP*GP*GP*CP*G)-3'), MAGNESIUM ION Authors: Chu, B, Paukstelis, P.J. Deposit date: 2018-08-30 Release date: 2018-11-14 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.57 Å) Cite: Crystal Structure of a Tetrameric DNA Fold-Back Quadruplex. J. Am. Chem. Soc., 140, 2018
6MC2	Crystal structure of a tetrameric DNA fold-back quadruplex Descriptor: DNA (5'-D(*CP*GP*TP*AP*AP*GP*GP*CP*G)-3'), MAGNESIUM ION Authors: Chu, B, Paukstelis, P.J. Deposit date: 2018-08-30 Release date: 2018-11-14 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.05 Å) Cite: Crystal Structure of a Tetrameric DNA Fold-Back Quadruplex. J. Am. Chem. Soc., 140, 2018
1EUI	ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN Descriptor: URACIL-DNA GLYCOSYLASE, URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN Authors: Ravishankar, R, Sagar, M.B, Roy, S, Purnapatre, K, Handa, P, Varshney, U, Vijayan, M. Deposit date: 1998-06-18 Release date: 1999-06-22 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (3.2 Å) Cite: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG. Nucleic Acids Res., 26, 1998
221D	INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA Descriptor: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3') Authors: Gao, Y.-G, Robinson, H, Van Boom, J.H, Wang, A.H.-J. Deposit date: 1995-06-26 Release date: 1996-01-31 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA. Biophys.J., 69, 1995
479D	CRYSTAL STRUCTURE A DNA:RNA HYBRID DUPLEX, A DYNAMIC MODEL FOR RNASE H RECOGNITION Descriptor: DNA (5'-D(*CP*TP*CP*TP*TP*CP*TP*TP*C)-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') Authors: Xiong, Y, Sundaralingam, M. Deposit date: 1999-07-08 Release date: 2000-05-15 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). Nucleic Acids Res., 28, 2000
5Z7D	p204HINab-dsDNA complex structure Descriptor: DNA (5'-D(P*CP*CP*AP*TP*CP*AP*GP*AP*AP*AP*GP*AP*GP*AP*GP*C)-3'), Interferon-activable protein 204 Authors: Jin, T, Jiang, J, Xiao, T.S. Deposit date: 2018-01-28 Release date: 2019-01-30 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (4.5 Å) Cite: Structural mechanism of DNA recognition by the p204 HIN domain. Nucleic Acids Res., 2021
5W7O	2-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant Descriptor: DNA (5'-D(*AP*TP*GP*(US3)P*CP*G)-3'), MAGNESIUM ION, RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'), ... Authors: Fang, Z, Yang, F, Huang, Z. Deposit date: 2017-06-20 Release date: 2017-06-28 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.75 Å) Cite: 2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant To Be Published
4C30	Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2 Descriptor: DNA HELICASE II, DNA STRAND FOR25, DNA STRAND REV25, ... Authors: Stelter, M, Acajjaoui, S, McSweeney, S, Timmins, J. Deposit date: 2013-08-21 Release date: 2013-10-30 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd. Plos One, 8, 2013
4KPY	DNA binding protein and DNA complex structure Descriptor: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'), DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), ... Authors: Sheng, G, Zhao, H, Wang, J, Rao, Y, Wang, Y. Deposit date: 2013-05-14 Release date: 2014-01-29 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (2.406 Å) Cite: Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc.Natl.Acad.Sci.USA, 111, 2014
4C2U	Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, Form 1 Descriptor: DNA HELICASE II, FOR25, GLYCEROL, ... Authors: Stelter, M, Acajjaoui, S, McSweeney, S, Timmins, J. Deposit date: 2013-08-20 Release date: 2013-10-30 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.55 Å) Cite: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd. Plos One, 8, 2013
1Q32	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase Descriptor: tyrosyl-DNA phosphodiesterase Authors: He, X, Babaoglu, K, Price, A, Nitiss, K.C, Nitiss, J.L, White, S.W. Deposit date: 2003-07-28 Release date: 2004-09-07 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.03 Å) Cite: Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison J.Mol.Biol., 372, 2007
4C2T	Crystal structure of full length Deinococcus radiodurans UvrD in complex with DNA Descriptor: DNA HELICASE II, DNA STRAND FOR28, DNA STRAND REV28, ... Authors: Stelter, M, Acajjaoui, S, McSweeney, S, Timmins, J. Deposit date: 2013-08-20 Release date: 2013-10-30 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (3.997 Å) Cite: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd. Plos One, 8, 2013
5US2	2-Se-T2-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant Descriptor: DNA (5'-D(*AP*(US3)P*GP*TP*CP*G)-3'), MAGNESIUM ION, RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'), ... Authors: Fang, Z, Yang, F, Huang, Z. Deposit date: 2017-02-13 Release date: 2017-03-08 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.9 Å) Cite: 2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant To Be Published
6DBW	Cryo-EM structure of RAG in complex with 12-RSS substrate DNA Descriptor: CALCIUM ION, Forward strand of 12-RSS substrate DNA, Recombination activating gene 1 - MBP chimera, ... Authors: Wu, H, Liao, M, Ru, H, Mi, W. Deposit date: 2018-05-03 Release date: 2018-08-01 Last modified: 2024-03-13 Method: ELECTRON MICROSCOPY (4.7 Å) Cite: DNA melting initiates the RAG catalytic pathway. Nat. Struct. Mol. Biol., 25, 2018
6DBX	Cryo-EM structure of RAG in complex with 12-RSS substrate DNA Descriptor: CALCIUM ION, Forward strand of 12-RSS substrate DNA, Recombination activating gene 1 - MBP chimera, ... Authors: Wu, H, Liao, M, Ru, H, Mi, W. Deposit date: 2018-05-03 Release date: 2018-08-01 Last modified: 2024-03-13 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: DNA melting initiates the RAG catalytic pathway. Nat. Struct. Mol. Biol., 25, 2018
6BRR	Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites Descriptor: DNA (25-MER), DNA (cytosine-5)-methyltransferase 3-like, DNA (cytosine-5)-methyltransferase 3A, ... Authors: Zhang, Z.M, Song, J. Deposit date: 2017-11-30 Release date: 2018-01-31 Last modified: 2024-12-25 Method: X-RAY DIFFRACTION (2.97 Å) Cite: Structural basis for DNMT3A-mediated de novo DNA methylation. Nature, 554, 2018

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