PDB: 46169 resultsInfo pagesStatus searchChemie searchBIRD

---

3JPO	Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochloromethylene triphosphate Descriptor: 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... Authors: Batra, V.K, Upton, J, Kashmerov, B, Beard, W.A, Wilson, S.H, Goodman, M.F, McKenna, C.E. Deposit date: 2009-09-04 Release date: 2010-06-02 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2 Å) Cite: Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc., 132, 2010
3JPQ	Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate Descriptor: 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... Authors: Batra, V.K, Upton, J, Kashmerov, B, Beard, W.A, Wilson, S.H, Goodman, M.F, McKenna, C.E. Deposit date: 2009-09-04 Release date: 2010-06-02 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc., 132, 2010
3M9M	Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion Descriptor: CALCIUM ION, CYTIDINE-5'-TRIPHOSPHATE, Cisplatin, ... Authors: Wong, J.H.Y, Ling, H. Deposit date: 2010-03-22 Release date: 2010-06-16 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. Embo J., 29, 2010
3M9O	Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion Descriptor: ADENOSINE-5'-TRIPHOSPHATE, CALCIUM ION, Cisplatin, ... Authors: Wong, J.H.Y, Ling, H. Deposit date: 2010-03-22 Release date: 2010-06-16 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2 Å) Cite: Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. Embo J., 29, 2010
3M9N	Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion Descriptor: CALCIUM ION, CYTIDINE-5'-TRIPHOSPHATE, Cisplatin, ... Authors: Wong, J.H.Y, Ling, H. Deposit date: 2010-03-22 Release date: 2010-06-16 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.93 Å) Cite: Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. Embo J., 29, 2010
4MZR	Crystal structure of a polypeptide p53 mutant bound to DNA Descriptor: Cellular tumor antigen p53, ZINC ION, consensus DNA anti-sense strand, ... Authors: Emamzadah, S.T, Tropia, L, Vincenti, I, Falquet, B, Halazonetis, T.D. Deposit date: 2013-09-30 Release date: 2014-01-15 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Reversal of the DNA-Binding-Induced Loop L1 Conformational Switch in an Engineered Human p53 Protein. J.Mol.Biol., 426, 2014
4H10	Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic Helix-Loop-Helix domains with E-box DNA Descriptor: Aryl hydrocarbon receptor nuclear translocator-like protein 1, Circadian locomoter output cycles protein kaput, E-box DNA antisense strand, ... Authors: Wang, Z, Su, X.-D. Deposit date: 2012-09-10 Release date: 2012-12-26 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.402 Å) Cite: Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA. Cell Res., 23, 2013
8EBS	Initial DNA-lesion (Cy5) binding by XPC and TFIIH Descriptor: CALCIUM ION, Centrin-2, DNA, ... Authors: Kim, J, Yang, W. Deposit date: 2022-08-31 Release date: 2023-04-19 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (4 Å) Cite: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature, 617, 2023
8EBW	Initial DNA-lesion (AP) binding by XPC and TFIIH complex2 Descriptor: CALCIUM ION, Centrin-2, DNA, ... Authors: Kim, J, Yang, W. Deposit date: 2022-08-31 Release date: 2023-04-19 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (5.6 Å) Cite: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature, 617, 2023
8EBV	Initial DNA-lesion (AP) binding by XPC and TFIIH complex 1 Descriptor: CALCIUM ION, Centrin-2, DNA, ... Authors: Kim, J, Yang, W. Deposit date: 2022-08-31 Release date: 2023-04-19 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (7.1 Å) Cite: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature, 617, 2023
8EBX	XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) Descriptor: CALCIUM ION, Centrin-2, DNA, ... Authors: Kim, J, Yang, W. Deposit date: 2022-08-31 Release date: 2023-04-19 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature, 617, 2023
2RDI	Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms Descriptor: DI(HYDROXYETHYL)ETHER, DNA polymerase IV, GLYCEROL Authors: Wong, J.H.Y, Ling, H. Deposit date: 2007-09-24 Release date: 2008-06-24 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (1.92 Å) Cite: Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4. J.Mol.Biol., 379, 2008
2W8L	Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3', 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... Authors: Eoff, R.L, Zhang, H, Egli, M, Guengerich, F.P. Deposit date: 2009-01-16 Release date: 2009-01-27 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (3 Å) Cite: Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts. J.Biol.Chem., 284, 2009
2W8K	Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in syn orientation Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3', 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... Authors: Eoff, R.L, Zhang, H, Egli, M, Guengerich, F.P. Deposit date: 2009-01-16 Release date: 2009-01-27 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts. J.Biol.Chem., 284, 2009
2W9A	Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dGTP Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3', 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... Authors: Eoff, R.L, Zhang, H, Kosekov, I.D, Rizzo, C.J, Egli, M, Guengerich, F.P. Deposit date: 2009-01-22 Release date: 2009-05-12 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem., 284, 2009
2W9B	Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA Descriptor: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOCP)-3', 5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', DNA POLYMERASE IV, ... Authors: Eoff, R.L, Zhang, H, Kosekov, I.D, Rizzo, C.J, Egli, M, Guengerich, F.P. Deposit date: 2009-01-22 Release date: 2009-05-12 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.28 Å) Cite: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem., 284, 2009
2W9C	Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP Descriptor: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3', 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', DNA POLYMERASE IV, ... Authors: Eoff, R.L, Zhang, H, Kosekov, I.D, Rizzo, C.J, Egli, M, Guengerich, F.P. Deposit date: 2009-01-22 Release date: 2009-05-12 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem., 284, 2009
102D	SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE Descriptor: 1,3-BIS(AMIDINOPHENOXY)PROPANE, DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3') Authors: Nunn, C.M, Neidle, S. Deposit date: 1994-12-15 Release date: 1995-02-07 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine. J.Med.Chem., 38, 1995
4IBU	Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R in sequence-specific complex with DNA Descriptor: 1,2-ETHANEDIOL, ACETATE ION, Cellular tumor antigen p53, ... Authors: Eldar, A, Rozenberg, H, Diskin-Posner, Y, Shakked, Z. Deposit date: 2012-12-09 Release date: 2013-08-14 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Res., 41, 2013
4IBW	Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R in sequence-specific complex with DNA Descriptor: 1,2-ETHANEDIOL, Cellular tumor antigen p53, DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'), ... Authors: Eldar, A, Rozenberg, H, Diskin-Posner, Y, Shakked, Z. Deposit date: 2012-12-09 Release date: 2013-08-14 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (1.791 Å) Cite: Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Res., 41, 2013
4IBV	Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation S240R in sequence-specific complex with DNA Descriptor: 1,2-ETHANEDIOL, Cellular tumor antigen p53, DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'), ... Authors: Eldar, A, Rozenberg, H, Diskin-Posner, Y, Shakked, Z. Deposit date: 2012-12-09 Release date: 2013-08-14 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Res., 41, 2013
7SU3	CryoEM structure of DNA-PK complex VII Descriptor: ADENOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3'), ... Authors: Chen, X, Liu, L, Gellert, M, Yang, W. Deposit date: 2021-11-16 Release date: 2022-01-12 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Autophosphorylation transforms DNA-PK from protecting to processing DNA ends. Mol.Cell, 82, 2022
2VA2	Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3', 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... Authors: Irimia, A, Pallan, P.S, Egli, M. Deposit date: 2007-08-28 Release date: 2007-10-30 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene. J.Biol.Chem., 282, 2007
3SWM	The NAC domain of ANAC019 in complex with DNA, gold derivative Descriptor: GOLD ION, NAC domain-containing protein 19, oligonucleotide forward, ... Authors: Welner, D, Lo Leggio, L. Deposit date: 2011-07-14 Release date: 2012-04-11 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (4.25 Å) Cite: DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors. Biochem.J., 444, 2012
3CFP	Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 1 Descriptor: CALCIUM ION, CHLORIDE ION, DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3'), ... Authors: Wang, J, Klimenko, D, Wang, M, Steitz, T.A, Konigsberg, W.H. Deposit date: 2008-03-04 Release date: 2009-03-10 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant To be Published

<129130131132133134135136137138139140141142143144>