Interaction mode
Mode:  H-Bb H-Mj S-Bb L-Bb L-Mn 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), helix(es) (H) with the major groove of DNA (Mj), 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
Histone
(PF00125.26)
1aoi 1eqz 1f66 1id3 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1u35 1zbb 1zla 2cv5 2f8n 2nqb 3a6n 3afa 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3c1b 3c1c 3kwq 3mvd 3o62 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1v 4kud 4qlc 4xzq 4ym5 4ys3 4z5t 4z66 5ay8 5b0y 5b0z 5b1l 5b1m 5b24 5b31 5b32 5b33 5cpk 5e5a 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5jrg 5wcu 5x0x 5x0y 5x7x 5xm0 5xm1 5y0c 5y0d 5z23 5z30 5z3o 5z3v 5zbx 6dzt 6e0c 6hkt 6j99 6jou 6jr0 6jr1 6jyl 6kvd 6kw3 6kw4 6la8 6la9 6m3v 6o1d 6om3 6pa7 6pwv 6pwx 6px1 6r90 6r91 6r93 6r94 6t79 6t7a 6t7c 6t90 6tda 6ugm 6uh5 6uxw 6v2k 6v92 6vz4 6x59 6x5a 6y5d 6y5e 7k5x 7k5y 7k61 7k63 244
Exc
(PF07825.13)
1rh6 2ief 2og0 6p0s 6p0u 6
Mob_Pre
(PF01076.21)
4lvi 4lvj 4lvk 4lvl 4lvm 5
IRF
(PF00605.19)
2irf 2o61 2o6g 2pi0 11
Trans_reg_C
(PF00486.30)
1gxp 4nhj 5ed4 5x5l 10
Rrf2
(PF02082.22)
4chu 4hf1 4hf2 6y42 7
MarR
(PF01047.24)
4aik 5hlg 5hlh 16
EBV-NA1
(PF02905.16)
1b3t 5t7x 6pw2 10
PhdYeFM_antitox
(PF02604.21)
4zm0 4zm2 3
Forkhead
(PF00250.20)
2c6y 5x07 2
GntR
(PF00392.23)
4u0y 5d4s 2
MarR_2
(PF12802.9)
3zpl 4
PadR
(PF03551.16)
6qua 2
MogR_DNAbind
(PF12181.10)
3fdq 2
Ets
(PF00178.24)
1yo5 1
DNA_topoisoIV
(PF00521.22)
2xcr 1
Phage_integrase
(PF00589.24)
1q3v 1
DM
(PF00751.20)
4yj0 1
RNase_HII
(PF01351.20)
3o3f 1
IBD
(PF10416.11)
1pp7 1
HTH_17
(PF12728.9)
6ama 1
MerR_1
(PF13411.8)
4r4e 1
HTH_Crp_2
(PF13545.8)
5trd 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 1kx4 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1u35 1zla 2cv5 2nqb 3b6g 3c1b 45
Lambda integrase-like, catalytic core
(d.163.1.1)
1kbu 1nzb 1ouq 1pvp 1pvq 1q3v 1xns 1xo0 2crx 2hof 3crx 4crx 14
Excisionase-like
(a.6.1.7)
1rh6 2ief 2og0 4
Interferon regulatory factor
(a.4.5.23)
2o6g 2pi0 3
Nuclear receptor
(g.39.1.2)
1ga5 1hlz 3
Replication initiation protein
(a.4.5.10)
1rep 1
ets domain
(a.4.5.21)
1yo5 1
PhoB-like
(a.4.6.1)
1gxp 2
MarR-like transcriptional regulators
(a.4.5.28)
1z9c 2
HNH-motif
(d.4.1.1)
1v14 1
Viral DNA-binding domain
(d.58.8.1)
1b3t 2
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