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)
3w97 3x1v 3tu4 5b0y 5xm1 3w99 3x1u 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 5b32 5xm0 5x7x 5b1l 5b1m 5b24 5b31 5b33 5jrg 5gxq 5gtc 5gt3 5gsu 5gse 5b0z 5ay8 4jjn 4kud 4qlc 4x23 4ym5 4ym6 4z5t 3mvd 3azn 3afa 3ayw 1m18 1m1a 2f8n 3azm 3azl 1p3a 1p3b 1p3g 1u35 2cv5 3azk 3azj 3av2 3av1 3aze 3a6n 3azg 3azi 3azf 86
zf-C4
(PF00105.17)
5cbx 5cby 5cbz 5cc0 2c7a 5cc1 2a66 5e69 5e6a 5e6d 5emq 1r4r 3g9j 2han 4umm 3g8u 3g6r 3g6p 4aa6 3e00 3dzy 3dzu 4cn7 4hn5 4hn6 1r4o 1hlz 5uan 5va0 1by4 5va7 1hcq 1dsz 1ga5 1kb4 2ff0 5krb 1r0n 5l0m 1lat 1r4i 1kb6 67
Ets
(PF00178.21)
3wtx 1bc7 4l18 5jvt 5e8i 3wtv 3wtu 3wts 1k7a 1k79 1k78 3wty 1mdm 3mfk 4bnc 3zp5 23
Forkhead
(PF00250.17)
2c6y 6el8 5x07 2a07 1vtn 3g73 3co6 3co7 3coa 14
HTH_3
(PF01381.21)
4x4i 4x4h 4x4g 4x4f 4x4e 4x4d 4x4c 4x4b 8
Arg_repressor
(PF01316.20)
3laj 2p5l 3ere 3fhz 3lap 21
Trans_reg_C
(PF00486.27)
4nhj 1gxp 4kny 4kfc 7
Penicillinase_R
(PF03965.15)
2d45 1xsd 1sax 5
HSF_DNA-bind
(PF00447.16)
3hts 5d5x 5d5v 4
RTP
(PF02334.15)
2efw 2dpu 2dpd 4
CENP-T_C
(PF15511.5)
1id3 4kud 4jjn 3
CBFD_NFYB_HMF
(PF00808.22)
5t5k 4g92 3
MarR
(PF01047.21)
1z9c 4aij 3
PPV_E2_C
(PF00511.16)
1jj4 2bop 2
IRF
(PF00605.16)
2o61 2pi0 2
Pou
(PF00157.16)
5wc9 2
IBD
(PF10416.8)
1pp8 2
HTH_27
(PF13463.5)
5kk1 2
zf-C2H2
(PF00096.25)
5k5j 1
RNase_HII
(PF01351.17)
3o3f 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 - 2019

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