PDB: 48855 resultsInfo pagesStatus searchChemie searchBIRD

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6NUA	DNA-protein crosslink between E. coli YedK and ssDNA containing an abasic site Descriptor: DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3'), SOS response-associated peptidase YedK Authors: Eichman, B.F, Amidon, K.M. Deposit date: 2019-01-31 Release date: 2019-06-26 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (1.64 Å) Cite: Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link. Nat.Struct.Mol.Biol., 26, 2019
3MLN	DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II) Descriptor: DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3'), Transcription factor COE1, ZINC ION Authors: Treiber, N, Treiber, T, Zocher, G, Grosschedl, R. Deposit date: 2010-04-17 Release date: 2010-12-01 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins Genes Dev., 24, 2010
6RKV	E. coli DNA Gyrase - DNA binding and cleavage domain in State 2 Descriptor: DNA Strand 1, DNA Strand 2, DNA gyrase subunit A, ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2019-04-30 Release date: 2019-11-06 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (4.6 Å) Cite: Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun, 10, 2019
4XRM	homodimer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, DNA (5'-D(P*AP*GP*CP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*G)-3'), DNA (5'-D(P*TP*CP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*GP*C)-3'), ... Authors: Morgunova, E, Jorma, A, Yin, Y, Nitta, K.R, Dave, K, Enge, M, Kivioja, T, Popov, A, Taipale, J. Deposit date: 2015-01-21 Release date: 2015-11-04 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (1.6 Å) Cite: DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature, 527, 2015
4NDY	Human MHF1-MHF2 DNA complex Descriptor: Centromere protein S, Centromere protein X, DNA (26-MER) Authors: Zhao, Q, Saro, D, Sachpatzidis, A, Sung, P, Xiong, Y. Deposit date: 2013-10-28 Release date: 2014-01-22 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (6.999 Å) Cite: The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes. Nat Commun, 5, 2014
4NE1	Human MHF1 MHF2 DNA complexes Descriptor: Centromere protein S, Centromere protein X, DNA (26-MER) Authors: Zhao, Q, Saro, D, Sachpatzidis, A, Sung, P, Xiong, Y. Deposit date: 2013-10-28 Release date: 2014-01-22 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (6.499 Å) Cite: The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes. Nat Commun, 5, 2014
6X70	Rev1-DNA Binary Complex Descriptor: DNA (5'-D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3'), DNA repair protein REV1, ... Authors: Weaver, T.M, Freudenthal, B.D. Deposit date: 2020-05-29 Release date: 2020-09-30 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Visualizing Rev1 catalyze protein-template DNA synthesis. Proc.Natl.Acad.Sci.USA, 117, 2020
3G6X	Ternary complex of DNA Polymerase iota:DNA:dGTP with an abasic site at the templating position Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA polymerase iota, MAGNESIUM ION, ... Authors: Nair, D.T, Aggarwal, A.K. Deposit date: 2009-02-09 Release date: 2009-05-12 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.08 Å) Cite: DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota. Structure, 17, 2009
8FAK	DNA replication fork binding triggers structural changes in the PriA DNA helicase that regulate the PriA-PriB replication restart pathway in E. coli Descriptor: DNA (5'-D(P*CP*AP*GP*AP*CP*TP*CP*AP*TP*TP*TP*AP*GP*CP*CP*CP*TP*TP*AP*TP*CP*CP*G)-3'), DNA (5'-D(P*CP*GP*GP*AP*TP*AP*AP*GP*GP*GP*CP*TP*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*A)-3'), DNA (5'-D(P*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3'), ... Authors: Duckworth, A.T, Ducos, P.L, McMillan, S.D, Satyshur, K.A, Blumenthal, K.H, Deorio, H.R, Larson, J.A, Sandler, S.J, Grant, T, Keck, J.L. Deposit date: 2022-11-28 Release date: 2023-05-10 Last modified: 2024-10-23 Method: ELECTRON MICROSCOPY (3.22 Å) Cite: Replication fork binding triggers structural changes in the PriA helicase that govern DNA replication restart in E. coli. Nat Commun, 14, 2023
4C8K	Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP Descriptor: ((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3', ... Authors: Betz, K, Malyshev, D.A, Lavergne, T, Welte, W, Diederichs, K, Romesberg, F.E, Marx, A. Deposit date: 2013-10-01 Release date: 2013-12-11 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.17 Å) Cite: Structural Insights Into DNA Replication without Hydrogen Bonds. J.Am.Chem.Soc., 135, 2013
4QCB	Protein-DNA complex of Vaccinia virus D4 with double-stranded non-specific DNA Descriptor: 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3', GLYCEROL, Uracil-DNA glycosylase Authors: Schormann, N, Banerjee, S, Ricciardi, R, Chattopadhyay, D. Deposit date: 2014-05-09 Release date: 2015-06-10 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.89 Å) Cite: Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase. BMC Struct. Biol., 15, 2015
1BNK	HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA Descriptor: DNA (5'-D(*GP*AP*CP*AP*TP*GP*YRRP*TP*TP*GP*CP*CP*T)-3'), DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3'), PROTEIN (3-METHYLADENINE DNA GLYCOSYLASE) Authors: Lau, A.Y, Schaerer, O.D, Samson, L, Verdine, G.L, Ellenberger, T. Deposit date: 1998-07-29 Release date: 1998-10-21 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell(Cambridge,Mass.), 95, 1998
6KZV	Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative Descriptor: DNA gyrase subunit B, ~{N}-[2-[[cyclohexyl(methyl)amino]methyl]phenyl]-2-oxidanylidene-1~{H}-quinoline-3-carboxamide Authors: Mima, M, Ushiyama, F. Deposit date: 2019-09-25 Release date: 2020-05-06 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. Acs Omega, 5, 2020
138D	A-DNA DECAMER D(GCGGGCCCGC)-HEXAGONAL CRYSTAL FORM Descriptor: DNA (5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3') Authors: Ramakrishnan, B, Sundaralingam, M. Deposit date: 1993-09-15 Release date: 1994-01-15 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures. Biochemistry, 32, 1993
137D	A-DNA DECAMER D(GCGGGCCCGC)-ORTHORHOMBIC CRYSTAL FORM Descriptor: DNA (5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3') Authors: Ramakrishnan, B, Sundaralingam, M. Deposit date: 1993-09-15 Release date: 1994-01-15 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures. Biochemistry, 32, 1993
7DCI	Crystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation Descriptor: DNA (5'-D(*GP*GP*GP*AP*AP*TP*AP*TP*TP*CP*CP*C)-3'), Heat shock factor protein 2, SODIUM ION Authors: Wei, L, Wei, L. Deposit date: 2020-10-26 Release date: 2021-07-14 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Crystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation To Be Published
3Q36	Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit Descriptor: DNA primase large subunit, FE (III) ION, IRON/SULFUR CLUSTER Authors: Agarkar, V.B, Babayeva, N.D, Tahirov, T.H. Deposit date: 2010-12-21 Release date: 2011-04-13 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Crystal structure of the C-terminal domain of human DNA primase large subunit: Implications for the mechanism of the primase - polymerase alpha switch. Cell Cycle, 10, 2011
4PCZ	Crystal structure of a complex between R247G LlFPG mutant and a THF containing DNA Descriptor: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'), Formamidopyrimidine-DNA glycosylase, ... Authors: Coste, F, Castaing, B. Deposit date: 2014-04-17 Release date: 2015-04-01 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Nucleic Acids Res., 42, 2014
6NY3	CasX ternary complex with 30bp target DNA Descriptor: CasX, DNA Non-target strand, DNA target strand, ... Authors: Liu, J.J, Orlova, N, Nogales, E, Doudna, J.A. Deposit date: 2019-02-10 Release date: 2019-02-27 Last modified: 2024-11-06 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature, 566, 2019
4PD2	Crystal structure of a complex between a C248GH LlFpg mutant and a THF containing DNA Descriptor: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'), Formamidopyrimidine-DNA glycosylase, ... Authors: Coste, F, Castaing, B. Deposit date: 2014-04-17 Release date: 2015-04-01 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.65 Å) Cite: Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Nucleic Acids Res., 42, 2014
1AXP	DNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 6 STRUCTURES Descriptor: DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC)) Authors: Gyi, J.I, Lane, A.N, Conn, G.L, Brown, T. Deposit date: 1997-10-17 Release date: 1998-04-22 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes. Biochemistry, 37, 1998
4BDP	CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES Descriptor: DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3'), DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3'), MAGNESIUM ION, ... Authors: Kiefer, J.R, Mao, C, Beese, L.S. Deposit date: 1997-11-17 Release date: 1999-01-13 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature, 391, 1998
1B4Y	STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN INTRAMOLECULAR DNA TRIPLE HELIX. Descriptor: DNA (H-Y5 TRIPLE HELIX) Authors: Van Dongen, M.J.P, Doreleijers, J.F, Van Der Marel, G.A, Van Boom, J.H, Hilbers, C.W, Wijmenga, S.S. Deposit date: 1998-12-30 Release date: 1999-09-13 Last modified: 2023-12-27 Method: SOLUTION NMR Cite: Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix. Nat.Struct.Biol., 6, 1999
3MDA	DNA polymerase lambda in complex with araC Descriptor: DNA (5'-D(*CP*AP*GP*TP*AP*CP*(CAR))-3'), DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3'), DNA (5'-D(P*GP*CP*CP*G)-3'), ... Authors: Garcia-Diaz, M, Murray, M, Kunkel, T, Chou, K.M. Deposit date: 2010-03-30 Release date: 2010-04-28 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.031 Å) Cite: Interaction between DNA Polymerase lambda and anticancer nucleoside analogs. J.Biol.Chem., 285, 2010
5W1R	Cryo-EM structure of DNAPKcs Descriptor: DNA-dependent protein kinase catalytic subunit Authors: Sharif, H, Li, Y, Wu, H. Deposit date: 2017-06-04 Release date: 2017-07-19 Last modified: 2025-05-21 Method: ELECTRON MICROSCOPY (4.4 Å) Cite: Cryo-EM structure of the DNA-PK holoenzyme. Proc. Natl. Acad. Sci. U.S.A., 114, 2017

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