PDB: 265 resultsInfo pagesStatus searchChemie searchBIRD

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4O0I	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA Descriptor: 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', DNA polymerase I, GLYCEROL, ... Authors: Jiang, S, Gan, J, Sun, H, Huang, Z. Deposit date: 2013-12-13 Release date: 2014-12-17 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.203 Å) Cite: Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA TO BE PUBLISHED
6XBU	polymerase domain of polymerase-theta Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3'), DNA polymerase theta, ... Authors: Chen, X, Pomerantz, R, Zhao, J. Deposit date: 2020-06-07 Release date: 2021-06-09 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (3.29 Å) Cite: Pol theta reverse transcribes RNA and promotes RNA-templated DNA repair. Sci Adv, 7, 2021
4YFU	Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP Descriptor: DNA polymerase, Primer DNA, SULFATE ION, ... Authors: Wu, E.Y. Deposit date: 2015-02-25 Release date: 2015-07-22 Last modified: 2022-04-13 Method: X-RAY DIFFRACTION (1.5 Å) Cite: The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure, 23, 2015
6UEU	Crystal structure of BF DNA polymerase F710Y mutant bound to tetrahydrofuran and dATP Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3'), ... Authors: Wu, E.Y, Beese, L.S. Deposit date: 2019-09-23 Release date: 2020-09-30 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase To Be Published
6DSU	Bst DNA polymerase I pre-insertion complex structure Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'), DNA (5'-D(P*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... Authors: Chim, N, Jackson, L.N, Chaput, J.C. Deposit date: 2018-06-14 Release date: 2018-10-31 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.98 Å) Cite: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife, 7, 2018
6DSX	Bst DNA polymerase I post-chemistry (n+1 with dATP soak) structure Descriptor: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'), DNA (5'-D(*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), DNA polymerase I, ... Authors: Chim, N, Jackson, L.N, Chaput, J.C. Deposit date: 2018-06-14 Release date: 2018-10-31 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.99 Å) Cite: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife, 7, 2018
2BDP	CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 9 BASE PAIRS OF DUPLEX DNA Descriptor: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*GP*C)-3'), DNA (5'-D(P*AP*GP*CP*AP*TP*CP*AP*TP*GP*C)-3'), MAGNESIUM ION, ... Authors: Kiefer, J.R, Mao, C, Beese, L.S. Deposit date: 1997-11-17 Release date: 1999-01-13 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature, 391, 1998
3EYZ	Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form) Descriptor: 5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)-3', 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3', DNA polymerase I, ... Authors: Warren, J.J, Wu, E.Y, Golosov, A.A, Karplus, M, Beese, L.S. Deposit date: 2008-10-22 Release date: 2009-11-10 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.1 Å) Cite: The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis. Structure, 18, 2010
3EZ5	Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form). Descriptor: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE, 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3', 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3', ... Authors: Warren, J.J, Wu, E.Y, Golosov, A.A, Karplus, M, Beese, L.S. Deposit date: 2008-10-22 Release date: 2009-11-10 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.9 Å) Cite: The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis. Structure, 18, 2010
4B9N	Structure of the high fidelity DNA polymerase I correctly bypassing the oxidative formamidopyrimidine-dA DNA lesion. Descriptor: 5'-D(*CP*AP*AP*(FAX)*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3', 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP*TP*TP)-3', DNA POLYMERASE, ... Authors: Gehrke, T.H, Lischke, U, Arnold, S, Schneider, S, Carell, T. Deposit date: 2012-09-05 Release date: 2013-04-17 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions. Nat.Chem.Biol., 9, 2013
4B9L	Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site. Descriptor: 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3', 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3', DNA POLYMERASE I, ... Authors: Gehrke, T.H, Lischke, U, Arnold, S, Schneider, S, Carell, T. Deposit date: 2012-09-05 Release date: 2013-04-17 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions. Nat.Chem.Biol., 9, 2013
4UQG	A new bio-isosteric base pair based on reversible bonding Descriptor: 5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3', 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3', DNA POLYMERASE, ... Authors: Tomas-Gamasa, M, Serdjukov, S, Su, M, Mueller, M, Carell, T. Deposit date: 2014-06-23 Release date: 2014-12-03 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (2 Å) Cite: "Post-it" type connected DNA created with a reversible covalent cross-link. Angew. Chem. Int. Ed. Engl., 54, 2015
7ZUS	Crystal structure of ternary complex of Pol theta polymerase domain Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3'), DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3'), ... Authors: Krajewski, W.W, Turnbull, A.P, Willis, S, Charles, M, Stockley, M, Heald, R.A. Deposit date: 2022-05-13 Release date: 2022-10-12 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.26 Å) Cite: Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta. J.Med.Chem., 65, 2022
7ZX1	Crystal structure of Pol theta polymerase domain in complex with compound 22 Descriptor: (2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide, 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3'), ... Authors: Krajewski, W.W, Turnbull, A.P, Willis, S, Charles, M, Stockley, M, Heald, R.A. Deposit date: 2022-05-19 Release date: 2022-10-12 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.829 Å) Cite: Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta. J.Med.Chem., 65, 2022
7ZX0	Crystal structure of Pol theta polymerase domain in complex with compound 5 Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, 2-[5-bromanyl-3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]oxy-~{N}-ethyl-~{N}-(3-methylphenyl)ethanamide, DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3'), ... Authors: Krajewski, W.W, Turnbull, A.P, Willis, S, Charles, M, Stockley, M, Heald, R.A. Deposit date: 2022-05-19 Release date: 2022-10-12 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.99 Å) Cite: Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta. J.Med.Chem., 65, 2022
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
3HP6	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch Descriptor: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, 5'-D(*AP*CP*GP*CP*CP*GP*TP*GP*AP*TP*CP*G)-3', 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DDG))-3', ... Authors: Wu, E.Y, Beese, L.S. Deposit date: 2009-06-03 Release date: 2010-06-23 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.81 Å) Cite: The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J.Biol.Chem., 286, 2011
3HPO	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S mutant bound to G:T mismatch Descriptor: 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3', 5'-D(P*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3', DNA polymerase I, ... Authors: Wu, E.Y, Beese, L.S. Deposit date: 2009-06-04 Release date: 2010-06-23 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.75 Å) Cite: The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J.Biol.Chem., 286, 2011
3HT3	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3', 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3', ... Authors: Wu, E.Y, Beese, L.S. Deposit date: 2009-06-11 Release date: 2010-07-14 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.7 Å) Cite: The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J.Biol.Chem., 286, 2011
6DSV	Bst DNA polymerase I post-chemistry (n+2) structure Descriptor: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'), DNA (5'-D(P*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), DNA polymerase I, ... Authors: Chim, N, Jackson, L.N, Chaput, J.C. Deposit date: 2018-06-14 Release date: 2018-10-31 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.99 Å) Cite: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife, 7, 2018
6DSW	Bst DNA polymerase I pre-chemistry (n) structure Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3'), DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... Authors: Chim, N, Jackson, L.N, Chaput, J.C. Deposit date: 2018-06-14 Release date: 2018-10-31 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.589 Å) Cite: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife, 7, 2018
6DSY	Bst DNA polymerase I post-chemistry (n+1) structure Descriptor: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'), DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), DNA polymerase I, ... Authors: Chim, N, Jackson, L.N, Chaput, J.C. Deposit date: 2018-06-14 Release date: 2018-10-31 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (1.98 Å) Cite: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife, 7, 2018
6P5C	Bacillus Fragment DNA polymerase mutant I716M Descriptor: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'), DNA polymerase I, ... Authors: Wu, E.Y. Deposit date: 2019-05-30 Release date: 2020-03-25 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.2 Å) Cite: The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase. DNA Repair (Amst.), 89, 2020
8E24	Human DNA polymerase theta in complex with allosteric inhibitor Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, 2-[2,4-bis(trifluoromethyl)phenyl]-N-phenyl-N-[3-(pyridazin-3-yl)prop-2-yn-1-yl]acetamide, DNA, ... Authors: Mader, P, Pau, V.P.T, Sicheri, F. Deposit date: 2022-08-13 Release date: 2022-09-28 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.34 Å) Cite: Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta. J.Med.Chem., 65, 2022

 

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