3D-footprint cannot reliably estimate the specificity of 'Nucleic acid-binding proteins', as they bind to single-stranded DNA and thus accumulate more base contacts.

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updated Tue Jul 29 14:56:27 2025

structure name	CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS
reference	White et al. 'EMBO 20 5207 2001
source	SACCHAROMYCES CEREVISIAE
experiment	X-ray (resolution=3.10, R-factor=?)
structural superfamily	Histone-fold;lambda repressor-like DNA-binding domains;p53-like transcription factors;Nucleic acid-binding proteins;P-loop containing nucleoside triphosphate hydrolases;
reference complex	1id3_E 5o9g_F 6ftx_B 6r8y_H 6x0n_f 7e9c_D 7e9c_G 7nkx_f 7u0g_M 7vdt_B 7xcr_F 7xzx_N 7xzz_N 8xgc_4
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1id3_A interface=3,28,46, phRykpgtvalreirrfqkstellirkLpfqrlvreiaqdfktdlRfqssaigalqesveaylvslfedtnlaaihakrvtiqkkeiklarrlrger > 1id3_B interface=22, dniqgitkpairrlarrggvkRisgliyeevravlksflesvirdsvtytehakrktvtsldvvyalkrqgrtlygfgg > 1id3_C interface=28, qsrsakagltfpvgrvhrllrrgnyaqRigsgapvyltavleylaaeilelagnaardnkktriiprhlqlairnddelnkllgnvtiaqggvlpnihqnllpkksakat > 1id3_D interface=1, Rketyssyiykvlkqthpdtgisqksmsilnsfvndiferiateasklaaynkkstisareiqtavrlilpgelakhavsegtravtkyssst > 1id3_E interface=3,4,46, phRYkpgtvalreirrfqkstellirklpfqrlvreiaqdfktdlRfqssaigalqesveaylvslfedtnlaaihakrvtiqkkeiklarrlrger > 1id3_F interface=15, hrkilrdniqgitkPairrlarrggvkrisgliyeevravlksflesvirdsvtytehakrktvtsldvvyalkrqgrtlygfgg > 1id3_G interface= kasqsrsakagltfPvgrvhrllrrgnyaqrigsgapvyltavleylaaeilelagnaardnkktriiprhlqlairnddelnkllgnvtiaqggvlpnihqnllpkk > 1id3_H interface= vrketyssyiykvlKqthpdtgisqksmsilnsfvndiferiateasklaaynkkstisareiqtavrlilpgelakhavsegtravtkyssstqa