Interaction mode
Mode:  H-Bb S-Bb L-Bb L-Mn 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), β-strand(s) (S) with DNA backbone atoms (Bb), loop(s) (L) with DNA backbone atoms (Bb), loop(s) (L) with the minor groove of DNA (Mn).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
DNA_pol_B
(PF00136.23)
1q9x 2dtu 2dy4 2oyq 2xhb 3cfr 3k5l 3lzj 3nae 3ndk 3ne6 3qev 3rmb 3s9h 3si6 3snn 3spy 3spz 3sq0 3sun 3suo 3sup 3tab 3taf 4dtj 4dtm 4dto 4dtp 4dts 4dtx 4du3 4fj5 4fj7 4fj8 4fjh 4fjn 4fk0 4flv 4flw 4flx 4fly 4i9q 4khn 4khw 4m3u 4m3w 4m3x 4m3y 4m3z 4m41 4m42 4m45 5iud 5vu6 5vu7 5vu8 5vu9 6fwk 6g0a 6i8a 6qib 7kc0 70
Histone
(PF00125.26)
1aoi 1eqz 1f66 1p3i 1s32 1zbb 2cv5 2nqb 3azl 3tu4 4jjn 5b1l 5cpi 5gse 5wcu 5x0x 5z3o 5zbx 6dzt 6e0c 6e0p 6hkt 6iro 6iy2 6iy3 6jyl 6kiv 6kiw 6kiz 6m3v 6m44 6ne3 6nog 6nzo 6o1d 6o96 6om3 6pww 6px1 6px3 6r91 6r92 6r93 6r94 6t79 6t93 6x59 6xjd 6y5d 6y5e 7c0m 7crp 7crq 7k5x 7k5y 7k60 7k61 7k63 102
Toprim
(PF01751.24)
2rgr 2xkk 3k9f 3ltn 3rae 3raf 4fm9 4g0u 4g0v 4g0w 4j3n 4juo 4kpe 4kpf 4z2d 4z3o 4z4q 4z53 5bs8 5bta 5btc 5btd 5btg 5bti 5btl 5btn 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5gwi 5gwj 5gwk 5iwi 5zad 5zen 5zqf 6qx1 6z1a 73
DNA_pol_A
(PF00476.22)
1skr 1sl0 2ajq 2hhw 2hvh 2hvi 4ez9 5c51 6fbf 6p7e 11
DNA_pol_B_thumb
(PF14791.8)
4xa5 5iii 5iij 5j2b 5j2e 6ctm 6ctq 6g2q 8
DNA_ligase_OB_2
(PF14743.8)
2q2t 2q2u 6gdr 6rar 6ras 6rce 7
RVT_1
(PF00078.29)
6amo 6an8 6anq 6avt 4
IMS
(PF00817.22)
5ewf 5ewg 5l1k 3
DNA_pol3_alpha
(PF07733.14)
3e0d 3f2b 3f2c 3
CENP-T_C
(PF15511.8)
6jr0 6jr1 6r91 3
DNA_ligase_A_M
(PF01068.23)
2q2t 3l2p 2
rve
(PF00665.28)
5ejk 2
Linker_histone
(PF00538.21)
5wcu 1
Fapy_DNA_glyco
(PF01149.26)
4g4q 1
Viral_alk_exo
(PF01771.19)
3pov 1
Piwi
(PF02171.19)
5xq2 1
SAD_SRA
(PF02182.19)
3q0f 1
Exo_endo_phos
(PF03372.25)
4b5g 1
DNA_ligase_A_C
(PF04679.17)
1x9n 1
XPA_C
(PF05181.14)
5lcl 1
RPOL_N
(PF14700.8)
3e2e 1


SCOP domains
Note: this data is based only on structures available at the moment of the last SCOP release (2009)
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SCOP Domain Family PDB entries Number of structures
Nucleosome core histones
(a.22.1.1)
1eqz 1f66 1kx5 1p3i 1s32 1zbb 9
Prokaryotic DNA-bending protein
(a.55.1.1)
1ouz 1owf 1owg 2ht0 5
HNH-motif
(d.4.1.1)
1v14 1v15 3
Lambda integrase-like, catalytic core
(d.163.1.1)
1ma7 1pvr 2
Replication modulator SeqA, C-terminal DNA-binding domain
(d.228.1.1)
1lrr 1
© NPIDB team 2003 - 2021

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