Interaction mode
Mode:  H-Bb S-Bb L-Bb 
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).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
Histone
(PF00125.26)
1aoi 1eqz 1f66 1id3 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2cv5 2f8n 2fj7 2nqb 3a6n 3afa 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3c1b 3c1c 3kwq 3mvd 3o62 3tu4 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4g92 4jjn 4kud 4qlc 4x23 4xzq 4ym5 4ym6 4ys3 4z5t 4z66 5ay8 5b0y 5b0z 5b1l 5b1m 5b24 5b31 5b32 5b33 5cpi 5cpk 5e5a 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5wcu 5x0x 5x0y 5xm0 5xm1 5z23 5z30 5z3l 5z3o 5z3u 5z3v 5zbx 6dzt 6e0c 6e0p 6hkt 6iro 6iy2 6iy3 6j99 6jou 6jr0 6jyl 6k1p 6kiu 6kiv 6kiw 6kiz 6kvd 6kw3 6kw5 6kxv 6la8 6la9 6m3v 6m44 6m4d 6ne3 6nj9 6nog 6nqa 6nzo 6o1d 6o96 6om3 6pa7 6pwv 6pww 6pwx 6px1 6px3 6r8y 6r8z 6r90 6r91 6r92 6r93 6r94 6t79 6t7a 6t7b 6t7c 6t7d 6t90 6t93 6tda 6ugm 6uh5 6uxw 6v2k 6v92 6ven 6vz4 6x59 6x5a 6y36 6y37 6y5d 6y5e 6yov 7c0m 7cro 7crp 7crr 7k5x 7k5y 7k60 7k61 7k63 494
IMS
(PF00817.22)
1n48 1s0n 1s9f 2asd 2j6s 2j6u 2r8k 2uvu 2wtf 2xgp 3epg 3epi 3h4b 3jaa 3mfh 3mfi 3mr2 3mr3 3mr6 3ngd 3oha 3tq1 4dl6 4dl7 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed7 4ed8 4eey 4fs1 4gc6 4ir1 4ir9 4irc 4ird 4j9k 4j9l 4j9m 4j9n 4j9o 4j9s 4jv0 4o3n 4o3o 4o3p 4o3q 4o3r 4o3s 4q43 4q8e 4qwe 4rnm 4rnn 4ru9 4rzr 4yp3 4yqw 4yr0 4yr2 4yr3 5dg7 5dg8 5dg9 5dlf 5dlg 5dqg 5dqh 5ewe 5f9l 5f9n 5kfa 5kfb 5kfc 5kfd 5kfe 5kff 5kfg 5kfh 5kfi 5kfj 5kfk 5kfl 5kfm 5kfn 5kfo 5kfp 5kfq 5kfr 5kfs 5kft 5kfu 5kfv 5kfw 5kfx 5kfy 5kfz 5kg0 5kg1 5kg2 5kg3 5kg4 5kg5 5kg6 5kg7 5kt4 5kt5 5kt6 5kt7 5l1j 5l1l 5l9x 5yur 5yus 5yut 5yuu 5yuv 5yyd 5yye 6brx 6bs1 6d0z 6jul 6juo 6juq 6mp3 6mq8 6mxo 6pl7 6pl8 6plc 6pz3 6q02 6x70 156
CENP-T_C
(PF15511.8)
1aoi 1eqz 1f66 1id3 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3g 1p3i 1p3o 1p3p 1s32 1zbb 1zla 2cv5 2f8n 2nqb 3a6n 3afa 3av1 3av2 3azf 3azg 3azj 3azk 3azl 3c1b 3mvd 3tu4 3wkj 3x1t 3x1u 3x1v 4jjn 4kud 4xzq 4ym5 4z66 5b0z 5b1l 5b1m 5b31 5e5a 5gse 5wcu 5x0y 5x7x 5y0c 5y0d 5z3o 5z3u 5z3v 6hkt 6iro 6iy3 6j99 6jou 6jr0 6jr1 6jyl 6k1p 6kvd 6kw3 6kw4 6la8 6m44 6nj9 6om3 6pwv 6r94 6t79 6t7a 6t7c 6tda 6vz4 110
IMS_C
(PF11799.10)
1n56 1s10 1s97 1s9f 1t3n 2agq 2dpj 2ia6 2uvu 2uvv 2uvw 2w8k 2xgp 2xgq 3epg 3epi 3g6v 3g6y 3gqc 3gv5 3h4b 3khl 3m9n 3m9o 3mr5 3ngd 3pr5 3pw0 3pw5 3pw7 3tq1 4ebd 4ecz 4ed3 4ed7 4fbt 4ir1 4ir9 4irc 4ird 4jv0 4q43 4q44 4q8f 4qwd 4qwe 4r8u 4yr0 5dlf 5kfl 5kfm 5kfq 5kfw 5kt2 5kt3 5kt4 5kt5 5kt7 5ulw 5yut 5yv0 5yv2 6d0m 6d0z 6jup 6juq 6pl7 6pz3 6q02 81
RVT_connect
(PF06815.15)
1rtd 3kk3 3v6d 5txp 6amo 6an2 6an8 6anq 6asw 6avm 6avt 6ika 6uk0 13
zf-H2C2_2
(PF13465.8)
1tf3 2lt7 4f6m 4f6n 5vmu 5vmv 5vmw 5vmy 5vmz 6df8 6df9 6dfa 6ml2 13
DNA_pol_B
(PF00136.23)
2dy4 4flt 4flu 4flz 4fm0 4fm1 4fm2 6s1n 6s1o 9
Toprim
(PF01751.24)
3l4j 3l4k 3rad 4z53 5btc 5btd 5btf 8
DNA_ligase_A_M
(PF01068.23)
1x9n 2q2u 6gdr 6iml 6imn 6rau 8
NucS
(PF01939.18)
5gke 5gkf 5gkg 5gkh 5gki 7
DNA_pol_B_thumb
(PF14791.8)
4f5q 5j2c 5j2h 5tb9 6e3v 5
Cas_Cas1
(PF01867.18)
5ds6 5xvn 5xvo 7
Cas_Cas2CT1978
(PF09707.12)
5dqz 5ds6 5wfe 5
Transposase_1
(PF01359.20)
3hos 3hot 4r79 3
STAT_bind
(PF02864.17)
4y5w 5d39 5
Helicase_C
(PF00271.33)
6iro 6vz4 2
Linker_histone
(PF00538.21)
5wcu 7k5x 2
MutS_I
(PF01624.22)
1ewq 1fw6 2
HIN
(PF02760.17)
3rn2 3rn5 2
MutS_IV
(PF05190.20)
1wb9 3k0s 2
MutS_III
(PF05192.20)
1wb9 3k0s 2
CRISPR_Cas9_WED
(PF18061.3)
6m0x 6rjg 2
CBFD_NFYB_HMF
(PF00808.25)
5t5k 4
NTP_transf_2
(PF01909.25)
5xm8 2
ResIII
(PF04851.17)
6p4f 2
VRR_NUC
(PF08774.13)
5y7g 2
RQC
(PF09382.12)
2wwy 2
Cdh1_DBD_1
(PF18196.3)
5j70 2
zf-C4
(PF00105.20)
5va7 1
DNA_gyraseB
(PF00204.27)
5j5p 1
IN_DBD_C
(PF00552.23)
6u8q 1
XPG_I
(PF00867.20)
5kse 1
Endonuclease_NS
(PF01223.25)
6iid 1
RNase_HII
(PF01351.20)
4hht 1
SMC_N
(PF02463.21)
6zz6 1
Exo_endo_phos
(PF03372.25)
4b5g 1
Endonuclease_1
(PF04231.15)
1oup 1
RNA_pol_Rpb1_1
(PF04997.14)
6uq0 1
Phage_endo_I
(PF05367.13)
2pfj 1
zf-His_Me_endon
(PF05551.13)
1a73 1
DNA_pol3_alpha
(PF07733.14)
5fkw 1
Endonuc-EcoRV
(PF09233.13)
2rve 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 1id3 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1u35 1zbb 1zla 2cv5 2f8n 2fj7 2nqb 2nzd 2pyo 3b6f 3b6g 3c1b 3c1c 120
DNA repair protein MutS, domain I
(d.75.2.1)
1ewq 1fw6 2
MutY C-terminal domain-like
(d.113.1.3)
1rrq 1rrs 2
Replication initiation protein E1
(d.89.1.2)
1ksy 2
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