PDB: 45817 resultsInfo pagesStatus searchChemie searchBIRD

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3GYH	Crystal Structure Analysis of S. Pombe ATL in complex with damaged DNA containing POB Descriptor: 1-PYRIDIN-3-YLBUTAN-1-ONE, Alkyltransferase-like protein 1, DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3'), ... Authors: Tubbs, J.L, Arvai, A.S, Tainer, J.A, Shin, D.S. Deposit date: 2009-04-03 Release date: 2009-06-16 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature, 459, 2009
7S68	Structure of human PARP1 domains (Zn1, Zn3, WGR and HD) bound to a DNA double strand break. Descriptor: DNA (5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'), Fusion of PARP1 zinc fingers 1 and 3 (Zn1, Zn3), ... Authors: Rouleau-Turcotte, E, Pascal, J.M. Deposit date: 2021-09-13 Release date: 2022-06-29 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (3.3 Å) Cite: Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery. Mol.Cell, 82, 2022
4O5Y	O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine Descriptor: BARIUM ION, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), POTASSIUM ION Authors: Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. Deposit date: 2013-12-20 Release date: 2014-07-02 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.75 Å) Cite: O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine Acta Crystallogr.,Sect.D, 70, 2014
6IWV	Crystal structure of a single strand DNA binding protein Descriptor: Single-stranded DNA-binding protein 2 Authors: Wang, H.Y, Yan, X.X. Deposit date: 2018-12-07 Release date: 2019-08-14 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (1.52 Å) Cite: Crystal structure of the LUFS domain of human single-stranded DNA binding Protein 2 (SSBP2). Protein Sci., 28, 2019
2EX5	Group I Intron-encoded Homing Endonuclease I-CeuI Complexed With DNA Descriptor: CALCIUM ION, DNA endonuclease I-CeuI, I-CeuI DNA target site, ... Authors: Spiegel, P.C, Stoddard, B.L. Deposit date: 2005-11-07 Release date: 2006-05-23 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.2 Å) Cite: The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure, 14, 2006
278D	SUBSTITUTIONS AT C2' OF DAUNOSAMINE IN THE ANTICANCER DAUNORUBICIN ALTER ITS DNA-BINDING SEQUENCE SPECIFICITY Descriptor: 2'-BROMO-4'-EPIDAUNORUBICIN, DNA (5'-D(*CP*GP*(G49)P*CP*CP*G)-3' Authors: Gao, Y.-G, Priebe, W, Wang, A.H.-J. Deposit date: 1996-07-22 Release date: 1996-09-16 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Substitutions at C2' of daunosamine in the anticancer drug daunorubicin alter its DNA-binding sequence specificity. Eur.J.Biochem., 240, 1996
7NQF	Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 with dsDNA Descriptor: COBALT (II) ION, DNA(CGTGDG), TPR_REGION domain-containing protein Authors: Li, A.W.H, Doherty, A.J. Deposit date: 2021-03-01 Release date: 2022-05-04 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.02 Å) Cite: Molecular basis for the initiation of DNA primer synthesis. Nature, 605, 2022
8KGT	Structure of African swine fever virus topoisomerase II in complex with dsDNA Descriptor: ADENOSINE-5'-DIPHOSPHATE, DNA topoisomerase 2 Authors: Cong, J, Xin, Y, Li, X, Chen, Y. Deposit date: 2023-08-19 Release date: 2024-04-03 Last modified: 2024-08-14 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Structural insights into the DNA topoisomerase II of the African swine fever virus. Nat Commun, 15, 2024
6WK6	Crystal structure of human polymerase eta complexed with Xanthine containing DNA Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'), DNA (5'-D(*CP*AP*TP*(3ZO)P*CP*TP*CP*AP*CP*AP*CP*T)-3'), ... Authors: Jung, H, Lee, S. Deposit date: 2020-04-15 Release date: 2021-01-06 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.35 Å) Cite: Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase. Biochem.J., 477, 2020
1G55	Structure of human DNMT2, an enigmatic DNA methyltransferase homologue Descriptor: BETA-MERCAPTOETHANOL, DNA CYTOSINE METHYLTRANSFERASE DNMT2, GLYCEROL, ... Authors: Dong, A, Yoder, J.A, Zhang, X, Zhou, L, Bestor, T.H, Cheng, X. Deposit date: 2000-10-30 Release date: 2001-01-17 Last modified: 2018-06-13 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Nucleic Acids Res., 29, 2001
6GA0	Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with SNAP-Vista Green Descriptor: 5-[(4-methylphenyl)methylcarbamoyl]-2-(6-oxidanyl-3-oxidanylidene-4~{H}-xanthen-9-yl)benzoic acid, Methylated-DNA--protein-cysteine methyltransferase, SULFATE ION Authors: Miggiano, R, Rossi, F, Rizzi, M. Deposit date: 2018-04-11 Release date: 2018-05-09 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (2 Å) Cite: Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with a fluorescent probe. Biochem. Biophys. Res. Commun., 500, 2018
4O5X	O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine. Descriptor: 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), MAGNESIUM ION Authors: Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. Deposit date: 2013-12-20 Release date: 2014-07-02 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.6 Å) Cite: O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine Acta Crystallogr.,Sect.D, 70, 2014
1D83	STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION Descriptor: (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose, 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate, 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol, ... Authors: Gao, X, Mirau, P, Patel, D.J. Deposit date: 1992-07-22 Release date: 1993-07-15 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Structure refinement of the chromomycin dimer-DNA oligomer complex in solution. J.Mol.Biol., 223, 1992
1WAN	DNA DTA TRIPLEX, NMR, 7 STRUCTURES Descriptor: DNA (5'-D(*AP*GP*AP*TP*AP*GP*AP*AP*CP*CP*CP*CP*TP*TP*CP*TP*AP*TP*CP*TP*TP*AP*TP*AP*TP*CP*TP*(D3)P*TP*CP*TP*T)-3') Authors: Wang, E, Koshlap, K.M, Gillespie, P, Dervan, P.B, Feigon, J. Deposit date: 1996-01-14 Release date: 1996-07-11 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3. J.Mol.Biol., 257, 1996
8EVF	HUMAN DNA POLYMERASE ETA EXTENSION COMPLEX WITH AN INCOMING DCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*G)-3'), ... Authors: Pallan, P.S, Egli, M. Deposit date: 2022-10-20 Release date: 2023-08-02 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.87 Å) Cite: The peroxidation-derived DNA adduct, 6-oxo-M 1 dG, is a strong block to replication by human DNA polymerase eta. J.Biol.Chem., 299, 2023
8EVE	HUMAN DNA POLYMERASE ETA INSERTION COMPLEX Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, DI(HYDROXYETHYL)ETHER, ... Authors: Pallan, P.S, Egli, M. Deposit date: 2022-10-20 Release date: 2023-08-02 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.35 Å) Cite: The peroxidation-derived DNA adduct, 6-oxo-M 1 dG, is a strong block to replication by human DNA polymerase eta. J.Biol.Chem., 299, 2023
4O5W	O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine Descriptor: 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), MAGNESIUM ION, ... Authors: Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. Deposit date: 2013-12-20 Release date: 2014-07-02 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.6 Å) Cite: O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine Acta Crystallogr.,Sect.D, 70, 2014
4O5Z	O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine Descriptor: BARIUM ION, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), SODIUM ION Authors: Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. Deposit date: 2013-12-20 Release date: 2014-07-02 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.75 Å) Cite: O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine Acta Crystallogr.,Sect.D, 70, 2014
4Q8E	Human DNA polymerase eta inserting dCMPNPP opposite a phenanthriplatin adducted G Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, 5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3', 5'-D(*CP*AP*TP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3', ... Authors: Gregory, M.T, Yang, W. Deposit date: 2014-04-26 Release date: 2014-07-02 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.549 Å) Cite: Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Proc.Natl.Acad.Sci.USA, 111, 2014
1M5X	Crystal structure of the homing endonuclease I-MsoI bound to its DNA substrate Descriptor: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', CALCIUM ION, ... Authors: Chevalier, B, Turmel, M, Lemieux, C, Monnat, R.J, Stoddard, B.L. Deposit date: 2002-07-10 Release date: 2003-06-03 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.25 Å) Cite: Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI J.Mol.Biol., 329, 2003
4Q8F	Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, 5'-D(*AP*GP*TP*GP*TP*GP*AP*C)-3', 5'-D(*CP*AP*TP*CP*GP*TP*CP*AP*CP*AP*CP*T)-3', ... Authors: Gregory, M.T, Yang, W. Deposit date: 2014-04-26 Release date: 2014-07-02 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.797 Å) Cite: Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Proc.Natl.Acad.Sci.USA, 111, 2014
1T94	Crystal structure of the catalytic core of human DNA polymerase kappa Descriptor: polymerase (DNA directed) kappa Authors: Uljon, S.N, Johnson, R.E, Edwards, T.A, Prakash, S, Prakash, L, Aggarwal, A.K. Deposit date: 2004-05-14 Release date: 2004-08-31 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Crystal structure of the catalytic core of human DNA polymerase kappa. STRUCTURE, 12, 2004
8IBX	Structure of R2 with 3'UTR and DNA in unwinding state Descriptor: 3'UTR, DNA (60-MER), Reverse transcriptase-like protein, ... Authors: Deng, P, Tan, S, Wang, J, Liu, J.J. Deposit date: 2023-02-10 Release date: 2023-09-20 Method: ELECTRON MICROSCOPY (3.74 Å) Cite: Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon. Cell, 186, 2023
8IBW	Structure of R2 with 3'UTR and DNA in binding state Descriptor: 3'UTR, DNA (60-MER), Reverse transcriptase-like protein, ... Authors: Deng, P, Tan, S, Wang, J, Liu, J.J. Deposit date: 2023-02-10 Release date: 2023-09-20 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon. Cell, 186, 2023
5KE7	mouse Klf4 ZnF1-3 and TpG/MpA sequence DNA complex structure Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*(5CM)P*AP*CP*CP*TP*C)-3'), ... Authors: Hashimoto, H, Cheng, X. Deposit date: 2016-06-09 Release date: 2016-09-14 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.06 Å) Cite: Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res., 44, 2016

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