PDB: 47011 件ウェブページステータス検索Chemie searchBIRD

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6UOK	Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP 分子名称: 1,2-ETHANEDIOL, 8-OXO-GUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... 著者 Smith, M.R, Freudenthal, B.D. 登録日 2019-10-15 公開日 2020-01-08 最終更新日 2023-10-11 実験手法 X-RAY DIFFRACTION (2.55 Å) 主引用文献 Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta. J.Biol.Chem., 295, 2020
6UOM	Y271G DNA polymerase beta ternary complex with templating adenine and incoming r8-oxo-GTP 分子名称: 1,2-ETHANEDIOL, 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE, 8-OXO-GUANOSINE-5'-TRIPHOSPHATE, ... 著者 Smith, M.R, Freudenthal, B.D. 登録日 2019-10-15 公開日 2020-01-08 最終更新日 2023-10-11 実験手法 X-RAY DIFFRACTION (2.05 Å) 主引用文献 Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta. J.Biol.Chem., 295, 2020
6UOL	Y271G DNA polymerase beta substrate complex with a templating cytosine and incoming rGTP 分子名称: 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... 著者 Smith, M.R, Freudenthal, B.D. 登録日 2019-10-15 公開日 2020-01-08 最終更新日 2023-10-11 実験手法 X-RAY DIFFRACTION (1.936 Å) 主引用文献 Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta. J.Biol.Chem., 295, 2020
5SZT	Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP 分子名称: 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP, ACETATE ION, DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ... 著者 Hottin, A, Betz, K, Marx, A. 登録日 2016-08-15 公開日 2016-12-14 最終更新日 2024-01-17 実験手法 X-RAY DIFFRACTION (1.8 Å) 主引用文献 Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides. Chemistry, 23, 2017
6E3V	Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP 分子名称: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine, DNA (5'-D(*CP*CP*GP*AP*CP*(A38) P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... 著者 Koag, M.-C, Lee, S. 登録日 2018-07-15 公開日 2019-04-03 最終更新日 2023-10-11 実験手法 X-RAY DIFFRACTION (1.96 Å) 主引用文献 Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J. Am. Chem. Soc., 141, 2019
2VA2	Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand 分子名称: 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', ... 著者 Irimia, A, Pallan, P.S, Egli, M. 登録日 2007-08-28 公開日 2007-10-30 最終更新日 2023-12-13 実験手法 X-RAY DIFFRACTION (2.8 Å) 主引用文献 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
6E3W	Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP 分子名称: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*CP*GP*AP*CP*(A38) P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... 著者 Koag, M.-C, Lee, S. 登録日 2018-07-15 公開日 2019-04-03 最終更新日 2023-10-11 実験手法 X-RAY DIFFRACTION (2.02 Å) 主引用文献 Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J. Am. Chem. Soc., 141, 2019
4H10	Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic Helix-Loop-Helix domains with E-box DNA 分子名称: Aryl hydrocarbon receptor nuclear translocator-like protein 1, Circadian locomoter output cycles protein kaput, E-box DNA antisense strand, ... 著者 Wang, Z, Su, X.-D. 登録日 2012-09-10 公開日 2012-12-26 最終更新日 2024-02-28 実験手法 X-RAY DIFFRACTION (2.402 Å) 主引用文献 Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA. Cell Res., 23, 2013
6U6B	Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink with Manganese in the active site 分子名称: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, Cisplatin, DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3'), ... 著者 Ouzon-Shubeita, H, Vilas, C.K, Lee, S. 登録日 2019-08-29 公開日 2020-09-09 最終更新日 2023-10-11 実験手法 X-RAY DIFFRACTION (3.108 Å) 主引用文献 Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion. Biochem.J., 477, 2020
8VFH	Ternary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC 分子名称: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(FAP))-3'), ... 著者 Oden, P.N, Ryan, B.J, Freudenthal, B.D. 登録日 2023-12-21 公開日 2024-05-08 最終更新日 2024-06-05 実験手法 X-RAY DIFFRACTION (2.01 Å) 主引用文献 Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta. Nucleic Acids Res., 52, 2024
8VFD	Ternary DNA Polymerase Beta bound to DNA containing template FapydG incoming TTP analog 分子名称: 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione, DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... 著者 Oden, P.N, Ryan, B.J, Freudenthal, B.D. 登録日 2023-12-21 公開日 2024-05-08 最終更新日 2024-06-05 実験手法 X-RAY DIFFRACTION (2.1 Å) 主引用文献 Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta. Nucleic Acids Res., 52, 2024
8VFI	Ternary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dA 分子名称: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... 著者 Oden, P.N, Ryan, B.J, Freudenthal, B.D. 登録日 2023-12-21 公開日 2024-05-15 最終更新日 2024-06-05 実験手法 X-RAY DIFFRACTION (1.77 Å) 主引用文献 Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta. Nucleic Acids Res., 52, 2024
6VDD	POL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP 分子名称: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3'), DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... 著者 Shuman, S, Goldgur, Y, Ghosh, S. 登録日 2019-12-24 公開日 2020-02-12 最終更新日 2024-03-06 実験手法 X-RAY DIFFRACTION (1.9 Å) 主引用文献 Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme. Nucleic Acids Res., 48, 2020
5KTQ	LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP 分子名称: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, PROTEIN (DNA POLYMERASE I) 著者 Li, Y, Kong, Y, Korolev, S, Waksman, G. 登録日 1998-09-22 公開日 1998-09-30 最終更新日 2024-03-06 実験手法 X-RAY DIFFRACTION (2.5 Å) 主引用文献 Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Sci., 7, 1998
4RUA	Crystal structure of Y-family DNA polymerase Dpo4 bypassing a MeFapy-dG adduct 分子名称: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase IV, ... 著者 Patra, A, Banerjee, S, Stone, M.P, Egli, M. 登録日 2014-11-18 公開日 2015-08-05 最終更新日 2023-09-20 実験手法 X-RAY DIFFRACTION (3.07 Å) 主引用文献 Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV. J.Am.Chem.Soc., 137, 2015
4RUC	Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair 分子名称: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase IV, ... 著者 Patra, A, Banerjee, S, Stone, M.P, Egli, M. 登録日 2014-11-18 公開日 2015-08-05 最終更新日 2024-02-28 実験手法 X-RAY DIFFRACTION (2.9 Å) 主引用文献 Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV. J.Am.Chem.Soc., 137, 2015
6W2M	Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair at the primer terminus and flipped out dA 分子名称: CHLORIDE ION, DNA polymerase beta, Downstream Primer Strand, ... 著者 Batra, V.K, Wilson, S.H. 登録日 2020-03-06 公開日 2020-07-22 最終更新日 2023-10-18 実験手法 X-RAY DIFFRACTION (1.998 Å) 主引用文献 Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus. Commun Biol, 3, 2020
8OJB	HSV-1 DNA polymerase-processivity factor complex in exonuclease state active site 分子名称: CALCIUM ION, DNA (47-MER), DNA polymerase catalytic subunit 著者 Gustavsson, E, Grunewald, K, Elias, P, Hallberg, B.M. 登録日 2023-03-24 公開日 2024-04-03 最終更新日 2024-07-17 実験手法 ELECTRON MICROSCOPY (1.9 Å) 主引用文献 Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Nucleic Acids Res., 52, 2024
8OJC	HSV-1 DNA polymerase active site in alternative exonuclease state 分子名称: CALCIUM ION, DNA (47-MER), DNA polymerase catalytic subunit 著者 Gustavsson, E, Grunewald, K, Elias, P, Hallberg, B.M. 登録日 2023-03-24 公開日 2024-04-03 最終更新日 2024-07-17 実験手法 ELECTRON MICROSCOPY (2.08 Å) 主引用文献 Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Nucleic Acids Res., 52, 2024
8OJD	HSV-1 DNA polymerase beta-hairpin loop 分子名称: CALCIUM ION, DNA (47-MER), DNA (68-MER), ... 著者 Gustavsson, E, Grunewald, K, Elias, P, Hallberg, B.M. 登録日 2023-03-24 公開日 2024-04-03 最終更新日 2024-07-17 実験手法 ELECTRON MICROSCOPY (2.46 Å) 主引用文献 Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Nucleic Acids Res., 52, 2024
6JUQ	mutant PolIV-DNA incoming nucleotide complex 2 分子名称: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), ... 著者 Nair, D.T, Johnson, M.K. 登録日 2019-04-15 公開日 2020-02-19 最終更新日 2023-11-22 実験手法 X-RAY DIFFRACTION (2.74 Å) 主引用文献 A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res., 47, 2019
6JUP	Mutant PolIV-DNA incoming nucleotide complex 分子名称: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), ... 著者 Nair, D.T, Johnson, M.K. 登録日 2019-04-15 公開日 2020-02-19 最終更新日 2023-11-22 実験手法 X-RAY DIFFRACTION (2.44 Å) 主引用文献 A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res., 47, 2019
3D0A	Human p53 core domain with hot spot mutation R249S and second site suppressor mutation H168R in sequence-specific complex with DNA 分子名称: Cellular tumor antigen p53, DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3'), ZINC ION 著者 Suad, O, Rozenberg, H, Shakked, Z. 登録日 2008-05-01 公開日 2009-01-20 最終更新日 2023-11-01 実験手法 X-RAY DIFFRACTION (1.8 Å) 主引用文献 Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations J.Mol.Biol., 385, 2009
4MZR	Crystal structure of a polypeptide p53 mutant bound to DNA 分子名称: Cellular tumor antigen p53, ZINC ION, consensus DNA anti-sense strand, ... 著者 Emamzadah, S.T, Tropia, L, Vincenti, I, Falquet, B, Halazonetis, T.D. 登録日 2013-09-30 公開日 2014-01-15 最終更新日 2023-09-20 実験手法 X-RAY DIFFRACTION (2.9 Å) 主引用文献 Reversal of the DNA-Binding-Induced Loop L1 Conformational Switch in an Engineered Human p53 Protein. J.Mol.Biol., 426, 2014
5K5O	Structure of AspA-26mer DNA complex 分子名称: AspA, DNA (26-MER) 著者 Schumacher, M. 登録日 2016-05-23 公開日 2016-06-15 最終更新日 2023-09-27 実験手法 X-RAY DIFFRACTION (3.2 Å) 主引用文献 Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages. Science, 349, 2015

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