PDB: 46169 resultsInfo pagesStatus searchChemie searchBIRD

---

6U15	Human thymine DNA glycosylase N140A mutant bound to DNA with 2'-F-5-carboxyl-dC substrate analog Descriptor: DNA (28-MER), G/T mismatch-specific thymine DNA glycosylase Authors: Pidugu, L.S, Pozharski, E, Drohat, A.C. Deposit date: 2019-08-15 Release date: 2019-11-20 Last modified: 2023-11-15 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase. J.Am.Chem.Soc., 141, 2019
9F6K	Human DNA Polymerase epsilon bound to T-C mismatched DNA (Frayed Substrate state) Descriptor: DNA nascent strand, DNA polymerase epsilon catalytic subunit A, DNA template strand, ... Authors: Roske, J.J, Yeeles, J.T.P. Deposit date: 2024-05-01 Release date: 2024-08-07 Last modified: 2024-08-21 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon. Nat.Struct.Mol.Biol., 2024
9F6J	Human DNA Polymerase epsilon bound to T-C mismatched DNA (Polymerase Arrest state) Descriptor: DNA nascent strand, DNA polymerase epsilon catalytic subunit A, DNA template strand, ... Authors: Roske, J.J, Yeeles, J.T.P. Deposit date: 2024-05-01 Release date: 2024-08-07 Last modified: 2024-08-21 Method: ELECTRON MICROSCOPY (3.9 Å) Cite: Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon. Nat.Struct.Mol.Biol., 2024
5Y7G	Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap Descriptor: CALCIUM ION, DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3'), DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3'), ... Authors: Cho, Y, Jin, H. Deposit date: 2017-08-17 Release date: 2018-03-14 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (3.4 Å) Cite: Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease. J. Biol. Chem., 293, 2018
4X67	Crystal structure of elongating yeast RNA polymerase II stalled at oxidative Cyclopurine DNA lesions. Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Wang, L, Chong, J, Wang, D. Deposit date: 2014-12-07 Release date: 2015-02-04 Last modified: 2019-12-25 Method: X-RAY DIFFRACTION (4.1 Å) Cite: Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions. Proc.Natl.Acad.Sci.USA, 112, 2015
4X6A	Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Wang, L, Chong, J, Wang, D. Deposit date: 2014-12-07 Release date: 2015-02-04 Last modified: 2019-12-25 Method: X-RAY DIFFRACTION (3.96 Å) Cite: Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions. Proc.Natl.Acad.Sci.USA, 112, 2015
9C3T	Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTAAAC as recognition sequence Descriptor: DNA1, DNA2, Methyltransferase, ... Authors: Kottur, J, Quintana-Feliciano, R, Aggarwal, A.K. Deposit date: 2024-06-02 Release date: 2024-09-11 Last modified: 2024-09-25 Method: X-RAY DIFFRACTION (2.37 Å) Cite: Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. Nat Commun, 15, 2024
9C3U	Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTTTAC as recognition sequence Descriptor: DNA1, DNA2, Methyltransferase, ... Authors: Kottur, J, Quintana-Feliciano, R, Aggarwal, A.K. Deposit date: 2024-06-02 Release date: 2024-09-11 Last modified: 2024-09-25 Method: X-RAY DIFFRACTION (2.77 Å) Cite: Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. Nat Commun, 15, 2024
9C3S	Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTATAC as recognition sequence Descriptor: DNA1, DNA2, Methyltransferase, ... Authors: Kottur, J, Quintana-Feliciano, R, Aggarwal, A.K. Deposit date: 2024-06-02 Release date: 2024-09-11 Last modified: 2024-09-18 Method: X-RAY DIFFRACTION (2.16 Å) Cite: Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. Nat Commun, 15, 2024
4WX9	Crystal structure of Mycobacterium tuberculosis OGT in complex with DNA Descriptor: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'), GLYCEROL, ... Authors: Miggiano, R, Rossi, F, Garavaglia, S, Rizzi, M. Deposit date: 2014-11-13 Release date: 2015-11-04 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (3 Å) Cite: Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA. Biochem.J., 473, 2016
5CQK	Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B Descriptor: DNA dC->dU-editing enzyme APOBEC-3B, GLYCEROL, SODIUM ION, ... Authors: Shi, K, Kurahashi, K, Aihara, H. Deposit date: 2015-07-21 Release date: 2015-10-07 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.88 Å) Cite: Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J.Biol.Chem., 290, 2015
5CQI	Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B Descriptor: DNA dC-dU-editing enzyme APOBEC-3B, GLYCEROL, ZINC ION Authors: Shi, K, Kurahashi, K, Aihara, H. Deposit date: 2015-07-21 Release date: 2015-10-07 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (1.68 Å) Cite: Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J.Biol.Chem., 290, 2015
5CQD	Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B Descriptor: DNA dC->dU-editing enzyme APOBEC-3B, GLYCEROL, ZINC ION Authors: Shi, K, Kurahashi, K, Aihara, H. Deposit date: 2015-07-21 Release date: 2015-10-07 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.08 Å) Cite: Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J.Biol.Chem., 290, 2015
1V33	Crystal structure of DNA primase from Pyrococcus horikoshii Descriptor: DNA primase small subunit, PHOSPHATE ION, ZINC ION Authors: Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2003-10-25 Release date: 2004-03-23 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells, 8, 2003
6U82	Crystal Structure of the Double Homeodomain of DUX4 in Complex with a DNA aptamer containing bulge and loop Descriptor: DNA (38-MER), Double homeobox protein 4 Authors: Shi, K, Aihara, H. Deposit date: 2019-09-04 Release date: 2020-02-19 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.21 Å) Cite: DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. Faseb J., 34, 2020
6E93	Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 in complex with methylated DNA Descriptor: DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3'), ZINC ION, ... Authors: Hudson, N.O, Whitby, F.G, Buck-Koehntop, B.A. Deposit date: 2018-07-31 Release date: 2018-11-07 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.747 Å) Cite: Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J. Biol. Chem., 293, 2018
6E94	Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA Descriptor: DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3'), ZINC ION, ... Authors: Hudson, N.O, Whitby, F.G, Buck-Koehntop, B.A. Deposit date: 2018-07-31 Release date: 2018-11-07 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.594 Å) Cite: Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J. Biol. Chem., 293, 2018
4XIU	Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA containing TTT overhang Descriptor: DNA polymerase I, thermostable, MAGNESIUM ION, ... Authors: Wu, E.Y. Deposit date: 2015-01-07 Release date: 2015-01-21 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.5 Å) Cite: A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry, 54, 2015
7C17	The cryo-EM structure of E. coli CueR transcription activation complex with fully duplex promoter DNA Descriptor: DNA (72-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Fang, C.L, Zhang, Y. Deposit date: 2020-05-02 Release date: 2020-09-30 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (4.22 Å) Cite: CueR activates transcription through a DNA distortion mechanism. Nat.Chem.Biol., 17, 2021
1BBX	NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE Descriptor: DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3'), DNA-BINDING PROTEIN 7D Authors: Agback, P, Baumann, H, Knapp, S, Ladenstein, R, Hard, T. Deposit date: 1998-04-24 Release date: 1998-10-14 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Architecture of Nonspecific Protein-DNA Interactions in the Sso7D-DNA Complex Nat.Struct.Biol., 5, 1998
7Y43	Crystal structure of the KAT6A WH domain and its bound double stranded DNA Descriptor: DNA (5'-D(*GP*GP*AP*GP*TP*GP*CP*GP*CP*AP*CP*TP*CP*C)-3'), Histone acetyltransferase KAT6A, MAGNESIUM ION Authors: Wang, Z, Jia, Y. Deposit date: 2022-06-13 Release date: 2023-01-18 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (1.5 Å) Cite: The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Res., 51, 2023
4X0P	Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog Descriptor: 2',3'-dideoxyadenosine triphosphate, CALCIUM ION, DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'), ... Authors: Zahn, K.E, Doublie, S. Deposit date: 2014-11-21 Release date: 2015-03-18 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.911 Å) Cite: Human DNA polymerase theta grasps the primer terminus to mediate DNA repair. Nat.Struct.Mol.Biol., 22, 2015
4X0Q	Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3'), DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3'), ... Authors: Zahn, K.E, Doublie, S. Deposit date: 2014-11-22 Release date: 2015-03-18 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.9 Å) Cite: Human DNA polymerase theta grasps the primer terminus to mediate DNA repair. Nat.Struct.Mol.Biol., 22, 2015
1B3T	EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX Descriptor: DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)-3'), PROTEIN (NUCLEAR PROTEIN EBNA1) Authors: Bochkarev, A, Bochkareva, E, Edwards, A, Frappier, L. Deposit date: 1998-12-14 Release date: 1998-12-15 Last modified: 2023-08-09 Method: X-RAY DIFFRACTION (2.2 Å) Cite: The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1. J.Mol.Biol., 284, 1998
4WCG	The binding mode of Cyprinid Herpesvirus3 ORF112-Zalpha to Z-DNA Descriptor: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3'), ORF112, SULFATE ION Authors: Kus, K, Athanasiadis, A. Deposit date: 2014-09-04 Release date: 2015-11-18 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (1.5 Å) Cite: The Structure of the Cyprinid herpesvirus 3 ORF112-Z alpha Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response. J.Biol.Chem., 290, 2015

<34353637383940414243444546474849>