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
(PF00125.23)
4z5t 3x1v 5xm0 5x7x 3x1u 3tu4 3w97 3w99 3wa9 3wkj 3wtp 3x1s 3waa 3x1t 5xm1 4jjn 5b0z 5b1l 5b1m 5b24 5b31 5b32 5b33 5jrg 5gxq 5gsu 5gse 5b0y 5ay8 4kud 4qlc 4x23 4ym5 4ym6 3mvd 3azm 3av2 3av1 3afa 2f8n 2cv5 3ayw 3aze 3azn 3azk 3azj 3azl 3azi 3azg 3azf 1u35 1p3a 1m18 1p3b 5gt3 1p3g 3a6n 1m1a 86
zf-C4
(PF00105.17)
3g9j 5cbx 2c7a 5cby 5cbz 5cc0 5cc1 5e69 5e6a 1r4r 1r4o 2ff0 2han 4umm 3g8u 3g6r 3g6p 4aa6 3e00 3dzy 3dzu 4cn7 4hn5 4hn6 1r4i 1r0n 5e6d 5uan 1ga5 1hlz 1dsz 1by4 5l0m 5krb 1kb4 5emq 1hcq 1lat 1kb6 64
Ets
(PF00178.21)
1k78 1pue 1k7a 5jvt 1k79 1bc7 1mdm 5e8i 4l18 4bnc 3wts 3mfk 3zp5 3wtu 3wtv 3wtw 3wtx 3wty 25
HTH_3
(PF01381.21)
4x4b 4x4d 4x4c 4x4f 4x4e 4x4h 4yg4 4x4g 4x4i 9
Forkhead
(PF00250.17)
2c6y 2a07 1vtn 3g73 6el8 3co7 5x07 3co6 14
Trans_reg_C
(PF00486.27)
4kny 1gxp 4nhj 4kfc 2z33 5ed4 9
Arg_repressor
(PF01316.20)
3laj 3fhz 3lap 2p5l 3ere 20
HSF_DNA-bind
(PF00447.16)
5d5x 3hts 5d5v 4
RTP
(PF02334.15)
2dpu 2efw 2dpd 4
Penicillinase_R
(PF03965.15)
2d45 1sax 1xsd 4
CENP-T_C
(PF15511.5)
1id3 4kud 4jjn 3
CBFD_NFYB_HMF
(PF00808.22)
4g92 5t5k 3
IRF
(PF00605.16)
2o61 2pi0 2
MarR
(PF01047.21)
1z9c 4aij 2
MerR_1
(PF13411.5)
5i44 6
Pou
(PF00157.16)
5wc9 2
IBD
(PF10416.8)
1pp8 2
HTH_27
(PF13463.5)
5kk1 2
zf-C2H2
(PF00096.25)
5k5j 1
PPV_E2_C
(PF00511.16)
1jj4 1
RNase_HII
(PF01351.17)
3o3f 1
PhdYeFM_antitox
(PF02604.18)
4zm2 1
Exc
(PF07825.10)
2ief 1
HTH_17
(PF12728.6)
6amk 1
HTH_Crp_2
(PF13545.5)
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 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 - 2018

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