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
(PF00125.23)
3tu4 5b24 3c1c 3c1b 5b31 3azn 5b1m 3kwq 5b0z 3o62 3mvd 5b1l 3azh 3azg 3azf 5cpi 3aze 3ayw 3av2 3azi 3azm 5b32 3azl 3azk 5b33 3azj 5b0y 4qlc 3x1v 4xzq 3x1u 3x1t 4ym5 3x1s 4ym6 4x23 4kud 4jjn 3wtp 4ys3 3w99 3w98 4z66 5ay8 3w97 3wa9 3wkj 4z5t 3waa 1p3o 1p3i 1p3g 1p3f 1p3b 1p3a 5x0x 1p34 1p3k 5jrg 1p3m 1p3l 5x0y 1m18 1id3 5xm1 1f66 1eqz 1aoi 5xm0 1m1a 5x7x 1m19 5gse 2cv5 3a6n 5gt0 1zla 5gt3 5gsu 2f8n 2nqb 5e5a 2fj7 3afa 3av1 1p3p 5gxq 5gtc 1s32 233
CENP-T_C
(PF15511.5)
5gsu 3wkj 2cv5 2f8n 5gt0 1zla 1u35 5gtc 5gt3 5gse 3a6n 3afa 3av1 3av2 5e5a 2nqb 2fj7 3ayw 1s32 1m18 5xm0 5x7x 1m19 5x0y 1m1a 5xm1 1aoi 1eqz 1f66 1id3 5jrg 1p3m 1p3o 5gxq 1p3l 1p34 5x0x 1p3a 1p3k 5ay8 3waa 4z5t 4ys3 3wtp 3wa9 4z66 3tu4 3w98 3w99 4ym6 3x1s 4x23 3c1b 4jjn 4qlc 4kud 3x1v 4xzq 4ym5 3x1t 3x1u 3aze 3azk 5b33 5b32 3azl 5b31 3azn 3azj 3azf 3azg 3azh 3mvd 5b0z 3o62 5b0y 5b1l 3kwq 5b24 3c1c 5b1m 161
IMS_C
(PF11799.7)
4q43 4ir9 4r8u 4ir1 3gqc 4irc 4q45 1t3n 4q44 4ird 5c5j 4irk 19
IMS
(PF00817.19)
4ir1 4q43 4qwe 4irc 4ird 4gc6 1s9f 9
Cas_Cas1
(PF01867.15)
5dlj 5xvo 5xvn 5dqz 5ds6 5wfe 12
Cas_Cas2CT1978
(PF09707.9)
5wfe 5dqz 5ds6 5
Toprim
(PF01751.21)
5btc 5btf 5btd 4
DNA_topoisoIV
(PF00521.19)
5bs3 5iwi 3
MutS_I
(PF01624.19)
1fw6 1ewq 2
HIN
(PF02760.14)
3rn5 3rn2 2
RVT_connect
(PF06815.12)
1rtd 3kk3 2
CBFD_NFYB_HMF
(PF00808.22)
5t5k 4
VRR_NUC
(PF08774.10)
5y7g 2
zf-C4
(PF00105.17)
5va7 1
RNase_HII
(PF01351.17)
4hht 1
Transposase_1
(PF01359.17)
4r79 1
Exo_endo_phos
(PF03372.22)
5dfh 1
DNA_pol_B_thumb
(PF14791.5)
4jwn 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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