PDB: 45953 resultsInfo pagesStatus searchChemie searchBIRD

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6S58	AvaII restriction endonuclease in the absence of nucleic acids Descriptor: CALCIUM ION, Type II site-specific deoxyribonuclease, UNKNOWN ATOM OR ION Authors: Kisiala, M, Kowalska, M, Korza, H, Czapinska, H, Bochtler, M. Deposit date: 2019-06-30 Release date: 2020-05-20 Last modified: 2024-01-24 Method: X-RAY DIFFRACTION (2.32 Å) Cite: Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation. Nucleic Acids Res., 48, 2020
2Q7U	Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate Descriptor: IMIDO DIPHOSPHATE, MAGNESIUM ION, Protein traI, ... Authors: Lujan, S.A, Redinbo, M.R. Deposit date: 2007-06-07 Release date: 2008-05-20 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (3 Å) Cite: Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc.Natl.Acad.Sci.Usa, 104, 2007
3RTV	Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA Descriptor: (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'), 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, ... Authors: Marx, A, Diederichs, K, Betz, K. Deposit date: 2011-05-04 Release date: 2012-05-30 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.9 Å) Cite: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat.Chem.Biol., 8, 2012
8B4K	Rfa1-N-terminal domain in complex with phosphorylated Ddc2 Descriptor: Replication factor A protein 1 Authors: Yates, L.A, Zhang, X. Deposit date: 2022-09-20 Release date: 2023-09-27 Method: X-RAY DIFFRACTION (1.55 Å) Cite: A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A. Proc.Natl.Acad.Sci.USA, 120, 2023
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
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
8C7T	Unliganded transcriptional pleiotropic repressor CodY from Enterococcus faecalis Descriptor: GTP-sensing transcriptional pleiotropic repressor CodY Authors: Hainzl, T, Sauer-Eriksson, A.E. Deposit date: 2023-01-17 Release date: 2023-06-28 Last modified: 2023-11-15 Method: X-RAY DIFFRACTION (2.21 Å) Cite: Structural insights into CodY activation and DNA recognition. Nucleic Acids Res., 51, 2023
1IXC	Crystal structure of CbnR, a LysR family transcriptional regulator Descriptor: LysR-type regulatory protein Authors: Muraoka, S, Okumura, R, Ogawa, N, Miyashita, K, Senda, T. Deposit date: 2002-06-18 Release date: 2003-06-18 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend J.Mol.Biol., 328, 2003
1IZ1	CRYSTAL STRUCTURE OF CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR Descriptor: LysR-type regulatory protein Authors: Muraoka, S, Okumura, R, Ogawa, N, Miyashita, K, Senda, T. Deposit date: 2002-09-18 Release date: 2003-05-06 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend J.Mol.Biol., 328, 2003
4XR0	Escherichia Coli Replication Terminator Protein (Tus) Complexed With DNA- G/T mismatch. Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*GP*T)-3'), DNA (5'-D(*AP*TP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3'), ... Authors: Oakley, A.J. Deposit date: 2015-01-20 Release date: 2015-08-26 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Replisome speed determines the efficiency of the Tus-Ter replication termination barrier. Nature, 525, 2015
6VGD	Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Descriptor: Core-binding factor subunit beta, DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'), DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3'), ... Authors: Hou, C, Tsodikov, O.V. Deposit date: 2020-01-07 Release date: 2020-11-25 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.2 Å) Cite: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Structure, 29, 2021
8FTJ	Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosylase bound to DNA duplex containing urea Descriptor: 1,2-ETHANEDIOL, DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3'), DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3'), ... Authors: Tomar, R, Sharma, P, Harp, J.M, Egli, M, Stone, M.P. Deposit date: 2023-01-12 Release date: 2023-04-26 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase. Nucleic Acids Res., 51, 2023
5C8E	Crystal structure of Thermus thermophilus CarH bound to adenosylcobalamin and a 26-bp DNA segment Descriptor: 26-mer DNA segment containing the CarH operator sequence (antisense strand), 26-mer DNA segment containing the CarH operator sequence (sense strand), 5'-DEOXYADENOSINE, ... Authors: Jost, M, Drennan, C.L. Deposit date: 2015-06-25 Release date: 2015-09-30 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.89 Å) Cite: Structural basis for gene regulation by a B12-dependent photoreceptor. Nature, 526, 2015
6VGG	Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC Descriptor: Core-binding factor subunit beta, DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'), DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3'), ... Authors: Hou, C, Rohr, J, Tsodikov, O.V. Deposit date: 2020-01-08 Release date: 2020-11-25 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.31 Å) Cite: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Structure, 29, 2021
8UH7	Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Descriptor: ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Primer DNA strand, ... Authors: Gee, C.L, Marcus, K, Kelch, B.A, Makino, D.L. Deposit date: 2023-10-07 Release date: 2023-12-13 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.628 Å) Cite: Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM. Nat.Struct.Mol.Biol., 31, 2024
8UNF	Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Descriptor: ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Sliding clamp, ... Authors: Huang, Y, Marcus, K, Subramanian, S, Gee, L.C, Gorday, K, Ghaffari-Kashani, S, Luo, X, Zhang, L, O'Donnell, M, Subramanian, S, Kuriyan, J. Deposit date: 2023-10-18 Release date: 2023-12-13 Last modified: 2024-04-03 Method: ELECTRON MICROSCOPY (3.15 Å) Cite: Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM. Nat.Struct.Mol.Biol., 31, 2024
6VGE	Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Descriptor: Core-binding factor subunit beta, DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'), DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3'), ... Authors: Hou, C, Tsodikov, O.V. Deposit date: 2020-01-07 Release date: 2020-11-25 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.25 Å) Cite: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Structure, 29, 2021
5FDK	Crystal structure of RecU(D88N) in complex with palindromic DNA duplex Descriptor: Holliday junction resolvase RecU, palindromic DNA Authors: Khavnekar, S, Rafferty, J.B, Kale, A. Deposit date: 2015-12-16 Release date: 2016-12-07 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (3.208 Å) Cite: Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state. Nucleic Acids Res., 45, 2017
4YWM	Pyrococcus furiosus MCM N-terminal domain beta-turn triple mutant pentameric ring Descriptor: Cell division control protein 21, SULFATE ION, ZINC ION Authors: Froelich, C.A, Enemark, E.J. Deposit date: 2015-03-20 Release date: 2015-09-23 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.2 Å) Cite: MCM ring hexamerization is a prerequisite for DNA-binding. Nucleic Acids Res., 43, 2015
4YWK	Pyrococcus furiosus MCM N-terminal domain with Zinc-binding subdomain B deleted Descriptor: Cell division control protein 21 Authors: Froelich, C.A, Enemark, E.J. Deposit date: 2015-03-20 Release date: 2015-09-23 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.55 Å) Cite: MCM ring hexamerization is a prerequisite for DNA-binding. Nucleic Acids Res., 43, 2015
3SZ2	Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dG as templating nucleobase Descriptor: (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'), DNA polymerase I, ... Authors: Betz, K, Marx, A, Diederichs, K. Deposit date: 2011-07-18 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.15 Å) Cite: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat.Chem.Biol., 8, 2012
4YWL	Pyrococcus furiosus MCM N-terminal domain F179A point mutant pentameric ring Descriptor: Cell division control protein 21, SULFATE ION, ZINC ION Authors: Froelich, C.A, Enemark, E.J. Deposit date: 2015-03-20 Release date: 2015-09-23 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.2 Å) Cite: MCM ring hexamerization is a prerequisite for DNA-binding. Nucleic Acids Res., 43, 2015
3SV4	Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dT as templating nucleobase Descriptor: (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), DNA polymerase I, ... Authors: Betz, K, Diederichs, K, Marx, A. Deposit date: 2011-07-12 Release date: 2012-06-06 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.99 Å) Cite: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat.Chem.Biol., 8, 2012
7X8C	Crystal structure of a KTSC family protein from Euryarchaeon Methanolobus vulcani Descriptor: KTSC domain-containing protein, SODIUM ION Authors: Zhang, Z.F, Zhu, K.L, Chen, Y.Y, Cao, P, Gong, Y. Deposit date: 2022-03-12 Release date: 2022-08-17 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.73 Å) Cite: Biochemical and structural characterization of a KTSC family single-stranded DNA-binding protein from Euryarchaea. Int.J.Biol.Macromol., 216, 2022
4NLG	Y-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3', 5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3', ... Authors: Mukherjee, P, Wilson, R.C, Pata, J.D. Deposit date: 2013-11-14 Release date: 2014-01-22 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Three Residues of the Interdomain Linker Determine the Conformation and Single-base Deletion Fidelity of Y-family Translesion Polymerases. J.Biol.Chem., 289, 2014

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