Interaction mode
Mode:  H-Bb H-Mj S-Bb L-Bb 
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).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
Histone
(PF00125.26)
1m18 1m1a 1p3a 1p3b 1p3g 1u35 2cv5 2f8n 3a6n 3afa 3av1 3av2 3ayw 3aze 3azf 3azg 3azi 3azk 3azl 3azm 3azn 3mvd 3tu4 3w97 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4jjn 4kud 4qlc 4x23 4ym5 4ym6 4z5t 5ay8 5b0y 5b0z 5b1l 5b1m 5b24 5b31 5b32 5b33 5cpi 5gse 5gsu 5gt3 5gtc 5gxq 5jrg 5wcu 5x7x 5xm0 5xm1 5y0c 5y0d 5z23 5z3l 5z3u 5zbx 6e0p 6hkt 6j99 6jou 6jr0 6jr1 6kvd 6kw4 6kw5 6kxv 6la8 6la9 6m44 6m4d 6m4g 6m4h 6nzo 6o1d 6pa7 6pwx 6px3 6r8y 6r8z 6r90 6r92 6r93 6r94 6t90 6t93 6tda 6v2k 6v92 6vz4 6yov 7c0m 7crp 7crr 7k5x 7k60 162
CENP-T_C
(PF15511.8)
1eqz 1f66 1id3 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3m 1p3o 1p3p 1zbb 1zla 2fj7 2nqb 3a6n 3afa 3av1 3av2 3ayw 3azf 3azg 3azh 3azj 3azk 3azl 3azn 3c1b 3c1c 3kwq 3o62 3w97 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4jjn 4kud 4qlc 4x23 4xzq 4ym6 4ys3 4z66 5ay8 5b0y 5b1l 5b1m 5b24 5b31 5b32 5b33 5cpk 5e5a 5gsu 5gt0 5gt3 5gxq 5wcu 5x7x 5xm0 5y0c 5y0d 5z23 5z30 5z3l 5zbx 6e0p 6jou 6jr0 6jr1 6kvd 6kw3 6kw4 6kxv 6m4d 6nzo 6om3 6pa7 6pwx 6px3 6r91 6r92 6t79 6t7a 6t7c 6tda 6v2k 6v92 7k5x 113
zf-C4
(PF00105.20)
1a6y 1by4 1ga5 1hcq 1hlz 1kb4 1kb6 1lat 1r0n 1r4i 1r4o 1r4r 2c7a 2ff0 2nll 3cbb 3dzu 3dzy 3e00 3g6p 3g6r 3g8u 3g9i 3g9j 3g9o 3g9p 4aa6 4cn3 4cn5 4cn7 4hn5 4hn6 4iqr 4umm 5cbx 5cby 5cbz 5cc0 5cc1 5e69 5e6a 5e6d 5emc 5emp 5emq 5uan 5va0 5va7 6bqu 6bsf 6fbq 6fbr 6xwg 6xwh 87
Ets
(PF00178.24)
1awc 1bc7 1bc8 1dux 1k78 1k79 1k7a 1mdm 1pue 3mfk 3wts 3wtt 3wtu 3wtv 3wtw 3wtx 3wty 3wu1 3zp5 4bnc 4l18 4lg0 4uno 5e8i 5jvt 5ybd 6vg2 6vg8 6vgd 6vge 6vgg 7jsa 7jsl 46
Forkhead
(PF00250.20)
1vtn 2a07 2as5 2c6y 3co6 3co7 3coa 3g73 5x07 6ako 6el8 6nce 6ncm 6o3t 7cby 23
zf-H2C2_2
(PF13465.8)
1tf3 2lt7 5egb 5ei9 5vmx 6df5 6dfc 6jnl 6jnm 6v8u 11
Trans_reg_C
(PF00486.30)
1gxp 2z33 4kfc 4kny 4nhj 5ed4 8
Arg_repressor
(PF01316.23)
2p5l 3ere 3fhz 3laj 3lap 21
z-alpha
(PF02295.19)
1qbj 1sfu 2heo 3eyi 3irq 7
CBFD_NFYB_HMF
(PF00808.25)
5t5k 6y36 7c9o 4
RTP
(PF02334.18)
2dpd 2efw 3
PhdYeFM_antitox
(PF02604.21)
4zm2 6l8e 3
zf-C2H2
(PF00096.28)
6e93 6e94 2
MarR
(PF01047.24)
1z9c 4aij 2
Exc
(PF07825.13)
2ief 6p0u 2
HTH_Crp_2
(PF13545.8)
3n4m 5trd 2
MerR_1
(PF13411.8)
5i44 10
HSF_DNA-bind
(PF00447.19)
5d5x 2
PPV_E2_C
(PF00511.19)
1jj4 2
IBD
(PF10416.11)
1pp8 2
HTH_27
(PF13463.8)
5kk1 2
RNase_HII
(PF01351.20)
3o3h 1
Rrf2
(PF02082.22)
6y42 1
HIN
(PF02760.17)
4jbm 1
Penicillinase_R
(PF03965.18)
1sax 1
HTH_17
(PF12728.9)
6amk 1
zf-met
(PF12874.9)
6e94 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 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1u35 1zla 2cv5 2f8n 2fj7 2nqb 3c1b 3c1c 35
Nuclear receptor
(g.39.1.2)
1a6y 1by4 1dsz 1ga5 1hcq 1hlz 1kb2 1kb4 1kb6 1lat 1r0n 1r0o 1r4i 1r4o 2han 2nll 29
ets domain
(a.4.5.21)
1bc7 1k78 1k79 1k7a 1mdm 1pue 7
Replication terminator protein (RTP)
(a.4.5.7)
1f4k 2dpd 2efw 5
Interferon regulatory factor
(a.4.5.23)
2irf 2o6g 2pi0 6
HNH-motif
(d.4.1.1)
1pt3 1v14 1v15 6
Viral DNA-binding domain
(d.58.8.1)
1jj4 2bop 2
Penicillinase repressor
(a.4.5.39)
1sax 1xsd 2
Replication initiation protein
(a.4.5.10)
2nra 1
Heat-shock transcription factor
(a.4.5.22)
3hts 1
Excisionase-like
(a.6.1.7)
2ief 1
PhoB-like
(a.4.6.1)
1gxp 2
MarR-like transcriptional regulators
(a.4.5.28)
1z9c 1
39 kda initiator binding protein, IBP39, N-terminal domain
(a.4.5.44)
1pp8 2
© NPIDB team 2003 - 2021

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