4RDU
 
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4RBO
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6FVC
 | | Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants | | Descriptor: | Segmentation polarity homeobox protein engrailed | | Authors: | Trosanova, Z, Zachrdla, M, Jansen, S, Srb, P, Zidek, L, Kozelka, J. | | Deposit date: | 2018-03-02 | | Release date: | 2019-04-03 | | Last modified: | 2024-06-19 | | Method: | SOLUTION NMR | | Cite: | Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.
Phys Chem Chem Phys, 20, 2018
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3HDD
 | | ENGRAILED HOMEODOMAIN DNA COMPLEX | | Descriptor: | 5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3', 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3', ENGRAILED HOMEODOMAIN | | Authors: | Fraenkel, E, Rould, M.A, Chambers, K.A, Pabo, C.O. | | Deposit date: | 1998-07-13 | | Release date: | 1998-11-11 | | Last modified: | 2023-08-02 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures.
J.Mol.Biol., 284, 1998
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9ANT
 | | ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | | Descriptor: | ANTENNAPEDIA HOMEODOMAIN, DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), ... | | Authors: | Fraenkel, E, Pabo, C.O. | | Deposit date: | 1998-07-02 | | Release date: | 1998-10-14 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.
Nat.Struct.Biol., 5, 1998
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6M3D
 | | X-ray crystal structure of tandemly connected engrailed homeodomains (EHD) with R53A mutations and DNA complex | | Descriptor: | DNA (5'-D(*GP*GP*AP*TP*TP*AP*GP*GP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3'), SODIUM ION, ... | | Authors: | Sunami, T, Hirano, Y, Tamada, T, Kono, H. | | Deposit date: | 2020-03-03 | | Release date: | 2020-09-16 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural basis for designing an array of engrailed homeodomains.
Acta Crystallogr D Struct Biol, 76, 2020
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7DW5
 | | Crystal structure of DUX4 HD1-HD2 domain complexed with ERG sites | | Descriptor: | BROMIDE ION, DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3'), Double homeobox protein 4-like protein 2 | | Authors: | Zhang, H, Cheng, N, Li, Z, Zhang, W, Dong, X, Huang, J, Meng, G. | | Deposit date: | 2021-01-15 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.83 Å) | | Cite: | DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia.
Cancer Commun (Lond), 41, 2021
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3RKQ
 | | NKX2.5 Homeodomain dimer bound to ANF-242 DNA | | Descriptor: | ANF-242 DNA, Homeobox protein Nkx-2.5, MAGNESIUM ION | | Authors: | Genis, C, Scone, P, Kasahara, H, Nam, H.-J. | | Deposit date: | 2011-04-18 | | Release date: | 2012-05-09 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.
Biochemistry, 51, 2012
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3CMY
 | | Structure of a homeodomain in complex with DNA | | Descriptor: | 1,2-ETHANEDIOL, 5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC)-3', 5'-D(*DTP*DGP*DTP*DAP*DAP*DTP*DCP*DGP*DAP*DTP*DTP*DAP*DTP*DG)-3', ... | | Authors: | Birrane, G, Ladias, J.A.A, Soni, A. | | Deposit date: | 2008-03-24 | | Release date: | 2009-02-17 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural Basis for DNA Recognition by the Human PAX3 Homeodomain.
Biochemistry, 48, 2009
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4J19
 | | Structure of a novel telomere repeat binding protein bound to DNA | | Descriptor: | CHLORIDE ION, DNA (5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*A)-3'), ... | | Authors: | Kappei, D, Butter, F, Benda, C, Scheibe, M, Draskovic, I, Stevense, M, Lopes Novo, C, Basquin, C, Krastev, D.B, Kittler, R, Jessberger, R, Londono-Vallejo, A.J, Mann, M, Buchholz, F. | | Deposit date: | 2013-02-01 | | Release date: | 2013-05-29 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment.
Embo J., 32, 2013
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3ZOB
 | | Solution structure of chicken Engrailed 2 homeodomain | | Descriptor: | HOMEOBOX PROTEIN ENGRAILED-2 | | Authors: | Carlier, L, Balayssac, S, Cantrelle, F.X, Khemtemourian, L, Chassaing, G, Joliot, A, Lequin, O. | | Deposit date: | 2013-02-21 | | Release date: | 2013-08-28 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Investigation of Homeodomain Membrane Translocation Properties: Insights from the Structure Determination of Engrailed-2 Homeodomain in Aqueous and Membrane-Mimetic Environments.
Biophys.J., 105, 2013
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4XID
 | | AntpHD with 15bp DNA duplex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), ... | | Authors: | White, M.A, Zandarashvili, L, Iwahara, J. | | Deposit date: | 2015-01-06 | | Release date: | 2015-11-25 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.701 Å) | | Cite: | Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Biophys.J., 109, 2015
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5LTY
 | | Homeobox transcription factor CDX2 bound to methylated DNA | | Descriptor: | DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'), DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3'), Homeobox protein CDX-2 | | Authors: | Morgunova, E, Popov, A, Taipale, J. | | Deposit date: | 2016-09-07 | | Release date: | 2017-05-31 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (2.66 Å) | | Cite: | Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Science, 356, 2017
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5LUX
 | | Homeobox transcription factor CDX1 bound to methylated DNA | | Descriptor: | DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'), DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'), DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3'), ... | | Authors: | Morgunova, E, Popov, A, Taipale, J. | | Deposit date: | 2016-09-12 | | Release date: | 2017-05-17 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (3.23 Å) | | Cite: | Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Science, 356, 2017
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4UUT
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4XIC
 | | ANTPHD WITH 15BP di-thioate modified DNA DUPLEX | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)P*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), ... | | Authors: | White, M.A, Zandarashvili, L, Iwahara, J. | | Deposit date: | 2015-01-06 | | Release date: | 2015-11-25 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.69 Å) | | Cite: | Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Biophys.J., 109, 2015
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6WIG
 | | Structure of STENOFOLIA Protein HD domain bound with DNA | | Descriptor: | DNA (5'-D(P*CP*TP*TP*GP*AP*AP*TP*AP*AP*AP*TP*CP*AP*TP*TP*AP*AP*TP*TP*TP*GP*C)-3'), DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G)-3'), STENOFOLIA | | Authors: | Deng, J, Peng, S, Pathak, P. | | Deposit date: | 2020-04-09 | | Release date: | 2021-08-11 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA.
Acta Crystallogr D Struct Biol, 77, 2021
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5JLW
 | | AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7R)P*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), ... | | Authors: | White, M.A, Zandarashvili, L, Iwahara, J, Nguyen, D. | | Deposit date: | 2016-04-27 | | Release date: | 2016-06-22 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.088 Å) | | Cite: | Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.
Chembiochem, 17, 2016
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5HOD
 | | Structure of LHX4 transcription factor complexed with DNA | | Descriptor: | DNA (5'-D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3'), DNA (5'-D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3'), LIM/homeobox protein Lhx4 | | Authors: | Morgunova, E, Yin, Y, Popov, A, Taipale, J. | | Deposit date: | 2016-01-19 | | Release date: | 2017-02-01 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.682 Å) | | Cite: | Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Science, 356, 2017
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5JLX
 | | AntpHD with 15bp DNA duplex S-monothioated at Cytidine-8 | | Descriptor: | DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), Homeotic protein antennapedia, ... | | Authors: | White, M.A, Zandarashvili, L, Iwahara, J, Nguyen, D. | | Deposit date: | 2016-04-27 | | Release date: | 2016-06-22 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.748 Å) | | Cite: | Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.
Chembiochem, 17, 2016
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9B8U
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7PSX
 | | Structure of HOXB13 bound to hydroxymethylated DNA | | Descriptor: | DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'), DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3'), Homeobox protein Hox-B13, ... | | Authors: | Morgunova, E, Popov, A, Yin, Y, Taipale, J. | | Deposit date: | 2021-09-24 | | Release date: | 2022-10-05 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure of HOXB13 bound to hydroxymethylated DNA
To Be Published
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8BYX
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2VI6
 | | Crystal Structure of the Nanog Homeodomain | | Descriptor: | HOMEOBOX PROTEIN NANOG | | Authors: | Jauch, R, Ng, C.K.L, Saitakendu, K.S, Stevens, R.C, Kolatkar, P.R. | | Deposit date: | 2007-11-28 | | Release date: | 2008-01-15 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog.
J.Mol.Biol., 376, 2008
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7Q3O
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