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)
4x23 4qlc 4kud 4jjn 3x1s 3x1v 3wtp 3wkj 3waa 3wa9 3w99 3w97 3tu4 3x1t 3mvd 3x1u 3azn 2f8n 5b24 5b0z 5b0y 5ay8 4z5t 5b31 2cv5 1m18 1m1a 5b32 1p3a 1p3b 1p3g 1u35 5b33 4ym6 3ayw 3aze 3azf 3azg 3azi 3azj 3azk 3azl 3av2 3av1 3azm 4ym5 3a6n 3afa 72
zf-C4
(PF00105.17)
3g9j 2a66 3g6p 5cbx 5cby 5cbz 1r4r 1r4o 1r4i 1r0n 4umm 5cc1 2c7a 4hn6 4hn5 4cn7 2han 2ff0 4aa6 3g8u 3g6r 3e00 3dzy 1hlz 1hcq 5krb 5l0m 1ga5 1dsz 1by4 5cc0 1kb4 1kb6 1lat 5emq 3dzu 60
Ets
(PF00178.21)
3wtx 3wtw 3wtv 3wty 5jvt 5e8i 4l18 3zp5 4bnc 3wtu 1k78 1k79 1k7a 1pue 1bc7 1mdm 3mfk 3wts 3wtt 27
HTH_3
(PF01381.21)
4x4e 4x4i 4x4g 4x4f 4x4d 4x4c 4x4b 4x4h 8
Forkhead
(PF00250.17)
3coa 3co6 3g73 3co7 2a07 2c6y 1vtn 11
Trans_reg_C
(PF00486.27)
4kny 5ed4 2z33 1gxp 4nhj 4kfc 9
Arg_repressor
(PF01316.20)
3lap 2p5l 3fhz 3laj 3ere 20
HSF_DNA-bind
(PF00447.16)
5d5x 5d5v 3hts 4
RTP
(PF02334.15)
2efw 2dpu 2dpd 4
Penicillinase_R
(PF03965.15)
2d45 1sax 1xsd 4
CENP-T_C
(PF15511.5)
1id3 4kud 4jjn 3
IRF
(PF00605.16)
2pi0 2o61 2
MarR
(PF01047.21)
4aij 1z9c 2
MerR_1
(PF13411.5)
5i44 6
IBD
(PF10416.8)
1pp8 2
HTH_27
(PF13463.5)
5kk1 2
PPV_E2_C
(PF00511.16)
1jj4 1
CBFD_NFYB_HMF
(PF00808.22)
4g92 1
RNase_HII
(PF01351.17)
3o3f 1
PhdYeFM_antitox
(PF02604.18)
4zm2 1
Exc
(PF07825.10)
2ief 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 - 2017

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