PDB: 8861 resultsInfo pagesStatus searchChemie searchBIRD

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8B6K	The crystal structure of M644G variant of DNA Pol Epsilon containing dCTP in the polymerase active site Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA polymerase epsilon catalytic subunit A, ... Authors: Parkash, V, Johansson, E. Deposit date: 2022-09-27 Release date: 2023-10-25 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.5 Å) Cite: A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides. Nucleic Acids Res., 2023
8B67	The crystal structure of M644G variant of DNA Pol Epsilon containing CTP in the polymerase active site Descriptor: ACETATE ION, CALCIUM ION, CYTIDINE-5'-TRIPHOSPHATE, ... Authors: Parkash, V, Johansson, E. Deposit date: 2022-09-26 Release date: 2023-10-25 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.6 Å) Cite: A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides. Nucleic Acids Res., 2023
8B79	The crystal structure of M644G variant of DNA Pol Epsilon containing UTP in the polymerase active site Descriptor: ACETATE ION, CALCIUM ION, DNA polymerase epsilon catalytic subunit A, ... Authors: Parkash, V, Johansson, E. Deposit date: 2022-09-29 Release date: 2023-10-25 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.65 Å) Cite: A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides. Nucleic Acids Res., 2023
8B76	The crystal structure of M644G variant of DNA Pol Epsilon containing dTTP in the polymerase active site Descriptor: ACETATE ION, CALCIUM ION, DNA polymerase epsilon catalytic subunit A, ... Authors: Parkash, V, Johansson, E. Deposit date: 2022-09-28 Release date: 2023-11-01 Method: X-RAY DIFFRACTION (2.6 Å) Cite: A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides. Nucleic Acids Res., 2023
2HOJ	Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions Descriptor: MAGNESIUM ION, MANGANESE (II) ION, THIAMINE DIPHOSPHATE, ... Authors: Edwards, T.E, Ferre-D'Amare, A.R. Deposit date: 2006-07-14 Release date: 2006-09-19 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Structure, 14, 2006
6AR5	Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (Duplex Only) Descriptor: DNA, RNA Authors: Stamos, J.L, Lentzsch, A.M, Lambowitz, A.M. Deposit date: 2017-08-21 Release date: 2017-11-29 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.413 Å) Cite: Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications. Mol. Cell, 68, 2017
6Q4U	KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(DOC))-3'), ... Authors: Kropp, H.M, Diederichs, K, Marx, A. Deposit date: 2018-12-06 Release date: 2019-02-27 Last modified: 2024-01-24 Method: X-RAY DIFFRACTION (2.005 Å) Cite: The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide. Angew.Chem.Int.Ed.Engl., 58, 2019
4P36	Crystal structure of DJ-1 With Zn(II) bound (crystal 2) Descriptor: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL, Protein DJ-1, ZINC ION Authors: Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. Deposit date: 2014-03-05 Release date: 2014-04-09 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.182 Å) Cite: Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry, 53, 2014
4P35	Crystal structure of DJ-1 with Zinc(II) bound (crystal I) Descriptor: CHLORIDE ION, GLYCEROL, Protein DJ-1, ... Authors: Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. Deposit date: 2014-03-05 Release date: 2014-04-09 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.75 Å) Cite: Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry, 53, 2014
6WC5	Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA Complex Descriptor: Homeobox protein Nkx-2.5, Myocardin enhancer DNA, Myocyte-specific enhancer factor 2B Authors: Chen, L, Lei, X. Deposit date: 2020-03-29 Release date: 2020-07-22 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. J.Mol.Biol., 432, 2020
3ABD	Structure of human REV7 in complex with a human REV3 fragment in a monoclinic crystal Descriptor: DNA polymerase zeta catalytic subunit, Mitotic spindle assembly checkpoint protein MAD2B Authors: Hara, K, Hashimoto, H, Murakumo, Y, Kobayashi, S, Kogame, T, Unzai, S, Akashi, S, Takeda, S, Shimizu, T, Sato, M. Deposit date: 2009-12-07 Release date: 2010-02-16 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase {zeta} and REV1 J.Biol.Chem., 285, 2010
3ABE	Structure of human REV7 in complex with a human REV3 fragment in a tetragonal crystal Descriptor: DNA polymerase zeta catalytic subunit, Mitotic spindle assembly checkpoint protein MAD2B Authors: Hara, K, Hashimoto, H, Murakumo, Y, Kobayashi, S, Kogame, T, Unzai, S, Akashi, S, Takeda, S, Shimizu, T, Sato, M. Deposit date: 2009-12-07 Release date: 2010-02-16 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase {zeta} and REV1 J.Biol.Chem., 285, 2010
6ZY7	Cryo-EM structure of the entire Human topoisomerase II alpha in State 1 Descriptor: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside, DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3'), ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2020-07-30 Release date: 2021-05-26 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (4.64 Å) Cite: Structural basis for allosteric regulation of Human Topoisomerase II alpha. Nat Commun, 12, 2021
6ZY6	Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 2 Descriptor: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside, DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3'), ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2020-07-30 Release date: 2021-05-26 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (4.1 Å) Cite: Structural basis for allosteric regulation of Human Topoisomerase II alpha. Nat Commun, 12, 2021
6ZY8	Cryo-EM structure of the entire Human topoisomerase II alpha in State 2 Descriptor: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside, DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3'), ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2020-07-30 Release date: 2021-05-26 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (7.4 Å) Cite: Structural basis for allosteric regulation of Human Topoisomerase II alpha. Nat Commun, 12, 2021
6ZY5	Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 1 Descriptor: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside, DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3'), ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2020-07-30 Release date: 2021-05-26 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Structural basis for allosteric regulation of Human Topoisomerase II alpha. Nat Commun, 12, 2021
7TO2	Cryo-EM structure of RIG-I bound to the internal sites of p3SLR30 (+ATP) Descriptor: ADENOSINE-5'-DIPHOSPHATE, Antiviral innate immune response receptor RIG-I, MAGNESIUM ION, ... Authors: Wang, W, Pyle, A.M. Deposit date: 2022-01-22 Release date: 2022-11-02 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Mol.Cell, 82, 2022
4TUS	Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2) WITH MANGANESE IN THE ACTIVE SITE. Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, Cisplatin, DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2014-06-24 Release date: 2014-10-01 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.42 Å) Cite: Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta. J.Biol.Chem., 289, 2014
1NOY	DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX Descriptor: DNA (5'-D(*TP*TP*T)-3'), MANGANESE (II) ION, PROTEIN (DNA POLYMERASE (E.C.2.7.7.7)), ... Authors: Wang, J, Yu, P, Lin, T.C, Konigsberg, W.H, Steitz, T.A. Deposit date: 1996-02-16 Release date: 1996-10-14 Last modified: 2011-07-13 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Biochemistry, 35, 1996
6AOC	Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase Descriptor: 1,2-ETHANEDIOL, 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione, MANGANESE (II) ION, ... Authors: Kirby, K.A, Sarafianos, S.G. Deposit date: 2017-08-15 Release date: 2018-08-08 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H. Eur J Med Chem, 141, 2017
5XPO	Crystal structure of VDR-LBD complexed with 25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 Descriptor: (5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor Authors: Kato, A, Itoh, T, Yamamoto, K. Deposit date: 2017-06-03 Release date: 2018-06-06 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (2.28 Å) Cite: Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
5XPN	Crystal structure of VDR-LBD complexed with 25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 Descriptor: (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, ... Authors: Kato, A, Itoh, T, Yamamoto, K. Deposit date: 2017-06-03 Release date: 2018-07-11 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (1.96 Å) Cite: Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
5XPP	Crystal structure of VDR-LBD complexed with 25RS-(Hydroxyphenyl)-2-methylidene-19,26,27-trinor-1,25-dihydroxyvitamin D3 Descriptor: (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{ a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor Authors: Kato, A, Itoh, T, Yamamoto, K. Deposit date: 2017-06-03 Release date: 2018-06-06 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
5TBB	Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.39 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5TB9	Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)FTC-TP and Mn2+. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.49 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017

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