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 Wed Jul 30 11:56:32 2025

structure name	X-RAY CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE WITH ITS DNA SITE-SPECIFICALLY CROSSLINKED TO THE HISTONE OCTAMER
reference	Richmond et al. 'J. 430 45 2018
source	XENOPUS LAEVIS
experiment	X-ray (resolution=2.80, 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	5o9g_E 5o9g_F 5x0y_D 5x0y_G 5z3u_A 6ftx_B 6g0l_D 6iro_A 6nqa_A 6pww_K 6r25_E 6r8y_H 6x0n_f 6yov_C 7at8_D 7eg6_A 7egp_S 7nkx_a 7nkx_f 7otq_E 7u0g_M 7unc_a 7und_e 7vdt_B 7xcr_F 7xzx_N 7xzz_N 7zs9_e 8a3y_a 8aag_A 8atf_Q 8bvw_e 8byq_e 8ceo_r 8cww_A 8g57_E 8he5_a 8jh2_e 8jhf_A 8siy_G 8xgc_4
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5ong_A interface=1,27, HcyrpgtvalreirryqkstellirkLpfqrlvreiaqdfktdlrfqssavmalqeaseaylvalfedtnlaaihakrvtimpkdiqlarrirger > 5ong_B interface=8,21, niqgitkPairrlarrggvkRisgliyeetrgvlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg > 5ong_C interface= ktrssraGlqfpvgrvhrllRkgnyaervgagapvylaavleyltaeilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt > 5ong_D interface=3, ktRkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtkytsa > 5ong_E interface=3,27,45, hcYrpgtvalreirryqkstellirkLpfqrlvreiaqdfktdlRfqssavmalqeaseaylvalfedtnlaaihakrvtimpkdiqlarrirgera > 5ong_F interface= rkVlrdniqgitkpairrlarrggvkRisgliyeetrgvlkvflEnvirdavtytehakrktvtamdvvyalkrqgrtlygfgg > 5ong_G interface= akTrssraglqfpvgrvhrllrkgnyAervgagapvylaavleyLtaeilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkk > 5ong_H interface=2, tRkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtkytsa