PDB: 45953 resultsInfo pagesStatus searchChemie searchBIRD

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1PVG	Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II Descriptor: DNA topoisomerase II, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Authors: Classen, S, Olland, S, Berger, J.M. Deposit date: 2003-06-27 Release date: 2003-08-26 Last modified: 2017-10-11 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187 Proc.Natl.Acad.Sci.USA, 100, 2003
8H1G	The R406T mutant form of the Aquifex aeolicus MutL endonuclease domain Descriptor: CADMIUM ION, DI(HYDROXYETHYL)ETHER, DNA mismatch repair protein MutL, ... Authors: Fukui, K, Yano, T. Deposit date: 2022-10-03 Release date: 2023-08-16 Method: X-RAY DIFFRACTION (1.43 Å) Cite: Catalytic mechanism of the zinc-dependent MutL endonuclease reaction. Life Sci Alliance, 6, 2023
8H1F	Aquifex aeolicus MutL endonuclease domain complexed with zinc ions after soaking Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, DNA mismatch repair protein MutL, ... Authors: Fukui, K, Yano, T. Deposit date: 2022-10-03 Release date: 2023-08-16 Method: X-RAY DIFFRACTION (1.22 Å) Cite: Catalytic mechanism of the zinc-dependent MutL endonuclease reaction. Life Sci Alliance, 6, 2023
8H1E	Aquifex aeolicus MutL endonuclease domain complexed with manganese ions Descriptor: DI(HYDROXYETHYL)ETHER, DNA mismatch repair protein MutL, MANGANESE (II) ION Authors: Fukui, K, Yano, T. Deposit date: 2022-10-03 Release date: 2023-08-16 Method: X-RAY DIFFRACTION (1.22 Å) Cite: Catalytic mechanism of the zinc-dependent MutL endonuclease reaction. Life Sci Alliance, 6, 2023
8I50	Crystal structure of DNA octamer containing GuNA[Me,Me] Descriptor: DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3') Authors: Aoyama, H, Obika, S, Yamaguchi, T. Deposit date: 2023-01-21 Release date: 2023-08-09 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (0.95 Å) Cite: Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res., 51, 2023
8HU5	Crystal structure of DNA octamer containing GuNA[Me,tBu] Descriptor: DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3') Authors: Aoyama, H, Obika, H, Yamaguchi, T. Deposit date: 2022-12-22 Release date: 2023-08-09 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (0.93 Å) Cite: Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res., 51, 2023
1C11	INTERCALATED D(TCCCGTTTCCA) DIMER, NMR, 7 STRUCTURES Descriptor: DNA (5'-D(*TP*CP*CP*CP*GP*TP*TP*TP*CP*CP*A)-3') Authors: Gallego, J, Chou, S.H, Reid, B.R. Deposit date: 1998-07-15 Release date: 1998-07-22 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer. J.Mol.Biol., 273, 1997
7E8D	NSD2 E1099K mutant bound to nucleosome Descriptor: DNA (185-MER), Histone H2A type 1, Histone H2B type 1-J, ... Authors: Sengoku, T, Sato, K, Nishizawa, T, Nureki, O, Ogata, K. Deposit date: 2021-03-01 Release date: 2021-11-10 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (2.8 Å) Cite: Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2. Nat Commun, 12, 2021
4L0J	Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems Descriptor: DNA helicase I, MAGNESIUM ION, SULFATE ION Authors: Redzej, A, Ilangovan, A, Lang, S, Gruber, C.J, Topf, M, Zangger, K, Zechner, E.L, Waksman, G. Deposit date: 2013-05-31 Release date: 2013-06-19 Last modified: 2018-01-24 Method: X-RAY DIFFRACTION (1.85 Å) Cite: Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems. Mol.Microbiol., 89, 2013
6VSX	X-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD Descriptor: DNA helicase, PHOSPHATE ION Authors: Murakami, K.S, Chon, U. Deposit date: 2020-02-12 Release date: 2020-06-10 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (2 Å) Cite: Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. Nat Commun, 11, 2020
6WCK	KRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16. Descriptor: DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*(BRU)P*GP*TP*GP*GP*GP*AP*AP*(BRU)P*AP*GP*GP*GP*AP*A)-3'), POTASSIUM ION Authors: Schmidberger, J.W, Ou, A, Smith, N.M, Iyer, K.S, Bond, C.S. Deposit date: 2020-03-30 Release date: 2020-04-15 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (1.801 Å) Cite: High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A pi-stacking interactions for small-molecule recognition. Nucleic Acids Res., 48, 2020
6TR2	Pre-folded structures govern folding pathways of human telomeric G-quadruplexes Descriptor: DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3') Authors: Wang, B, Frelih, T, Plavec, J, Sket, P. Deposit date: 2019-12-17 Release date: 2020-01-01 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Pre-folded structures govern folding pathways of human telomeric G-quadruplexes. Nucleic Acids Res., 48, 2020
6AU4	Crystal structure of the major quadruplex formed in the human c-MYC promoter Descriptor: DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'), POTASSIUM ION Authors: Stump, S, Mou, T.C, Sprang, S.R, Natale, N.R, Beall, H.D. Deposit date: 2017-08-30 Release date: 2018-09-12 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.35 Å) Cite: Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene. PLoS ONE, 13, 2018
4ME3	1.8 Angstrom Crystal Structure of the N-terminal Domain of an Archaeal MCM Descriptor: DNA replication licensing factor MCM related protein, ZINC ION Authors: Fu, Y, Slaymaker, I.M, Wang, G, Chen, X.S. Deposit date: 2013-08-24 Release date: 2014-01-08 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.794 Å) Cite: The 1.8- angstrom Crystal Structure of the N-Terminal Domain of an Archaeal MCM as a Right-Handed Filament. J.Mol.Biol., 426, 2014
2LFX	Structure of the duplex when (5'S)-8,5'-cyclo-2'-deoxyguanosine is placed opposite dT Descriptor: DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*TP*GP*CP*AP*C)-3'), DNA (5'-D(*GP*TP*GP*CP*(2LF)P*TP*GP*TP*TP*TP*GP*T)-3') Authors: Huang, H, Das, R.S, Basu, A, Stone, M.P. Deposit date: 2011-07-18 Release date: 2012-06-27 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT. Chem.Res.Toxicol., 25, 2012
4H29	B-raf dimer DNA quadruplex Descriptor: DNA (5'-D(*GP*GP*GP*CP*GP*GP*GP*GP*AP*GP*GP*GP*GP*GP*AP*AP*GP*GP*GP*A)-3'), POTASSIUM ION Authors: Wei, D, Parkinson, G, Neidle, S. Deposit date: 2012-09-12 Release date: 2013-07-31 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.991 Å) Cite: Crystal Structure of a Promoter Sequence in the B-raf Gene Reveals an Intertwined Dimer Quadruplex. J.Am.Chem.Soc., 135, 2013
103D	THE UNUSUAL STRUCTURE OF THE HUMAN CENTROMERE (GGA)2 MOTIF: UNPAIRED GUANOSINE RESIDUES STACKED BETWEEN SHEARED G(DOT)A PAIRS Descriptor: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3') Authors: Chou, S.-H, Zhu, L, Reid, B.R. Deposit date: 1994-12-16 Release date: 1995-03-31 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs. J.Mol.Biol., 244, 1994
7KUL	DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G Descriptor: DIGUANOSINE-5'-TRIPHOSPHATE, DNA/RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*G)-3'), MAGNESIUM ION Authors: Fang, Z, Giurgiu, C, Szostak, J.W. Deposit date: 2020-11-25 Release date: 2021-09-08 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (1.64 Å) Cite: Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Angew.Chem.Int.Ed.Engl., 60, 2021
2LED	Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from intron of N-myc gene Descriptor: DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') Authors: Trajkovski, M, Plavec, J, Webba da Silva, M. Deposit date: 2011-06-15 Release date: 2012-03-14 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene. J.Am.Chem.Soc., 134, 2012
2LEE	Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from intron of N-myc gene Descriptor: DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') Authors: Trajkovski, M, Plavec, J, Webba da Silva, M. Deposit date: 2011-06-15 Release date: 2012-03-14 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene. J.Am.Chem.Soc., 134, 2012
8IEG	Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Descriptor: DNA (147-MER), E3 ubiquitin-protein ligase BRE1, Histone H2A type 1-B/E, ... Authors: Ai, H, Deng, Z, Pan, M, Liu, L. Deposit date: 2023-02-15 Release date: 2023-09-06 Last modified: 2023-09-20 Method: ELECTRON MICROSCOPY (3.44 Å) Cite: Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A. Mol.Cell, 83, 2023
3OZ5	S-Methyl Carbocyclic LNA Descriptor: DNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3'), SPERMINE Authors: Seth, P.R, Allerson, C.A, Berdeja, A, Siwkowski, A, Pallan, P.S, Gaus, H, Prakash, T.P, Watt, A.T, Egli, M, Swayze, E.E. Deposit date: 2010-09-24 Release date: 2010-11-24 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.36 Å) Cite: An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J.Am.Chem.Soc., 132, 2010
3V06	Crystal structure of S-6'-Me-3'-fluoro hexitol nucleic acid Descriptor: DNA (5'-D(*GP*CP*GP*TP*AP*(F5H)P*AP*CP*GP*C)-3'), STRONTIUM ION Authors: Pallan, P.S, Egli, M. Deposit date: 2011-12-07 Release date: 2012-02-08 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.53 Å) Cite: Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid. Biochemistry, 51, 2012
3V07	Crystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid Descriptor: DNA (5'-D(*GP*CP*GP*TP*AP*(F6H)P*AP*CP*GP*C)-3') Authors: Pallan, P.S, Egli, M. Deposit date: 2011-12-07 Release date: 2012-02-08 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.24 Å) Cite: Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid. Biochemistry, 51, 2012
3OZ4	R-Methyl Carbocyclic LNA Descriptor: DNA (5'-D(*GP*CP*GP*TP*AP*(URX)P*AP*CP*GP*C)-3') Authors: Seth, P.R, Allerson, C.A, Berdeja, A, Siwkowski, A, Pallan, P.S, Gaus, H, Prakash, T.P, Watt, A.T, Egli, M, Swayze, E.E. Deposit date: 2010-09-24 Release date: 2010-11-24 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.59 Å) Cite: An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J.Am.Chem.Soc., 132, 2010

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