Interaction mode
Mode:  H-Bb H-Mj L-Bb L-Mj 
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), loop(s) (L) with DNA backbone atoms (Bb), loop(s) (L) with the major groove of DNA (Mj).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
HTH_3
(PF01381.24)
1lli 1lmb 1per 1rio 1rpe 2or1 2r1j 3bdn 3clc 3cro 3jxb 3jxc 3jxd 3s8q 3u3w 3ufd 3zhm 3zkc 4ivz 4iwr 4pu3 4pu4 4x4b 4x4c 4x4d 4x4e 4x4f 4x4g 4x4h 4x4i 4yg1 4yg7 4z5c 4z5d 5jub 5k98 6chv 6fix 6jpi 6lb3 6w1a 104
Sigma70_r4
(PF04545.18)
1ku7 1rio 3iyd 3n97 4xln 4xlp 4xlq 4xlr 4xls 5tw1 5vi5 5vi8 6b6h 6c04 6cce 6ccv 6dcf 6edt 6ee8 6eec 6ido 6ldi 6m7j 6psq 6psr 6pss 6pst 6psu 6psw 6vvs 6vvt 6vvv 6vvx 6vvy 6vvz 6vw0 7c97 7chw 7ckq 7khc 47
zf-H2C2_2
(PF13465.8)
1a1h 1a1l 1aay 1f2i 1g2f 1llm 1p47 1tf6 1zaa 2i13 2prt 2wbs 3uk3 4is1 4r2s 4x9j 5eh2 5ke9 5kl2 5t0u 5v3j 5v3m 5wjq 5yef 5yeh 5yel 6b0p 6b0q 6b0r 6blw 47
TetR_N
(PF00440.25)
1jt0 4gcl 4gct 4i6z 4l62 4pxi 5dy0 5fmp 5gpc 5h58 5hbu 5k58 5ua1 5vl9 5yej 6c31 6en8 6gy3 6nsm 6nsn 6nsr 6o6p 63
HTH_8
(PF02954.21)
3iv5 3jr9 3jra 3jrb 3jrc 3jrd 3jre 3jrf 3jrg 3jrh 3jri 4fth 5ds9 5dtd 5e3l 5e3m 5e3n 5e3o 6p0s 6p0t 6p0u 41
LacI
(PF00356.23)
1cjg 1efa 1l1m 1lcd 1osl 1rzr 2bjc 2kei 2kej 2kek 2pe5 3oqm 3oqn 3oqo 7ce1 31
HTH_Crp_2
(PF13545.8)
1cgp 2cgp 3mzh 4i2o 5ciz 5x6d 5x6e 6pb4 6qwf 6qwh 6qwk 6qwm 28
Zn_clus
(PF00172.20)
1d66 1f4s 1f5e 1hwt 1pyi 1qp9 2er8 2ere 2erg 2hap 3coq 19
TFIIB
(PF00382.21)
1c9b 1d3u 4v1n 4v1o 5iy6 5iy8 5iy9 5iyc 5iyd 6o9l 12
RHD_DNA_bind
(PF00554.24)
1a3q 1gji 1le9 1ram 2i9t 2o61 2v2t 3gut 5u01 13
Pou
(PF00157.19)
1au7 1cqt 1hf0 1oct 2xsd 3l1p 5wc9 6t90 12
mTERF
(PF02536.16)
3mva 3mvb 3n6s 3n7q 5cky 5co0 5crj 5crk 8
Fe_dep_repress
(PF01325.21)
1c0w 1ddn 1f5t 1u8r 2isz 2it0 24
HTH_24
(PF13412.8)
3hos 3hot 4r79 4u7b 5hoo 11
Peptidase_S48
(PF03574.17)
4hri 4j00 4j01 4yrv 9
CUT
(PF02376.17)
2d5v 2o49 2o4a 6lff 4
TrmB
(PF01978.21)
5box 5bpd 5bpi 10
HTH_19
(PF12844.9)
4jcx 4jcy 4jqd 8
HTH_48
(PF17906.3)
3hos 3hot 5hoo 5
SoPB_HTH
(PF18090.3)
3mkw 3mky 3mkz 5
BamHI
(PF02923.17)
1bhm 2bam 3bam 4
Rap1-DNA-bind
(PF09197.12)
1ign 3ukg 4gfb 4
Homeodomain
(PF00046.31)
2h8r 6ryi 6u82 3
RNA_pol_Rpb1_1
(PF04997.14)
6alf 6alh 6asx 3
HVO_2753_ZBP
(PF07754.13)
5v3j 5v3m 5wjq 3
RAG1
(PF12940.9)
6oeo 6oep 6oeq 3
MarR
(PF01047.24)
5yi2 5yi3 12
Flp_N
(PF03930.16)
1m6x 1p4e 6
KORA
(PF16509.7)
2w7n 5clv 6
Phage_int_SAM_6
(PF18644.3)
5jjv 5jk0 6
GntR
(PF00392.23)
1hw2 4p9u 5
Phage_integrase
(PF00589.24)
5jjv 5jk0 5
LexA_DNA_bind
(PF01726.18)
3jso 3jsp 4
HNF-1_N
(PF04814.15)
1ic8 2h8r 4
zf-C4
(PF00105.20)
1r0o 3g8x 2
GATA
(PF00320.29)
1gat 1gau 2
ARID
(PF01388.23)
1kqq 2oeh 2
zf-CXXC
(PF02008.22)
5vc9 5w9s 2
FOXP-CC
(PF16159.7)
5kl2 5kl4 2
HTH_17
(PF12728.9)
6ama 4
zf-C2H2
(PF00096.28)
5k5l 2
HTH_1
(PF00126.29)
4iht 2
Forkhead
(PF00250.20)
2a07 2
Rep_3
(PF01051.23)
2z9o 2
Trp_repressor
(PF01371.21)
1rcs 2
Phage_CII
(PF05269.13)
1zs4 2
KorB
(PF08535.12)
1r71 2
Spo0A_C
(PF08769.13)
1lq1 2
HTH_Tnp_Mu_2
(PF09039.13)
4fcy 2
P22_Cro
(PF14549.8)
6on0 2
Telomere_res
(PF16684.7)
2v6e 2
Type_ISP_C
(PF18135.3)
4xqk 2
HLH
(PF00010.28)
1a0a 1
DNA_methylase
(PF00145.19)
6w8w 1
Myb_DNA-binding
(PF00249.33)
1h89 1
LIM
(PF00412.24)
5yel 1
HSF_DNA-bind
(PF00447.19)
5d5v 1
Topoisom_I
(PF01028.22)
2h7f 1
FUR
(PF01475.21)
4rb3 1
MethyltransfD12
(PF02086.17)
1yfj 1
TFIIF_beta
(PF02270.17)
5fmf 1
RTP
(PF02334.18)
2efw 1
HTH_7
(PF02796.17)
2gm4 1
RNA_pol_A_CTD
(PF03118.17)
6n4c 1
HTH_Tnp_Tc5
(PF03221.18)
1hlv 1
Sigma54_DBD
(PF04552.15)
5ui5 1
Put_DNA-bind_N
(PF06971.15)
3ikt 1
Recombinase
(PF07508.15)
4kis 1
CRISPR_Cas2
(PF09827.11)
5xvp 1
BpuJI_N
(PF11564.10)
5hlt 1
MarR_2
(PF12802.9)
4fx4 1
HTH_27
(PF13463.8)
5k1y 1
Myb_DNA-bind_6
(PF13921.8)
2kdz 1
ORC4_C
(PF14629.8)
5zr1 1
MqsA_antitoxin
(PF15731.7)
3o9x 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
Classic zinc finger, C2H2
(g.37.1.1)
1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l 1aay 1f2i 1jk1 1jk2 1llm 1p47 1tf6 1un6 1zaa 2drp 2gli 39
GalR/LacI-like bacterial regulator
(a.35.1.5)
1jfs 1jft 1jh9 1pnr 1qp0 1qp7 1qpz 1qqa 1vpw 1zay 2pua 2pub 2puc 2pud 2pue 2pug 16
Phage repressors
(a.35.1.2)
1lli 1lmb 1per 1rio 1rpe 2or1 2r1j 3cro 16
Rel/Dorsal transcription factors, DNA-binding domain
(b.2.5.3)
1a3q 1le9 1ooa 1ram 2i9t 2o61 2v2t 8
Zn2/Cys6 DNA-binding domain
(g.38.1.1)
1d66 1hwt 1pyi 1qp9 1zme 2hap 3coq 10
CAP C-terminal domain-like
(a.4.5.4)
1cgp 1ruo 1zrc 1zrd 1zre 7
Iron-dependent repressor protein
(a.4.5.24)
1c0w 1ddn 1f5t 1u8r 17
Replication initiation protein
(a.4.5.10)
1rep 2nra 2z9o 4
lambda integrase-like, N-terminal domain
(a.60.9.1)
1flo 1m6x 1p4e 11
Myb/SANT domain
(a.4.1.3)
1h89 1msf 2
POU-specific domain
(a.35.1.1)
1cqt 1ic8 3
Trp repressor, TrpR
(a.4.12.1)
1co0 1rcs 2
Zinc finger design
(k.12.1.1)
1g2f 2i13 3
DNA-binding domain of rap1
(a.4.1.6)
1ign 4
GntR-like transcriptional regulators
(a.4.5.6)
1hw2 1
Transcription factor IIB (TFIIB), core domain
(a.74.1.2)
1d3u 1
DNA repair glycosylase, 2 C-terminal domains
(a.96.1.3)
1diz 1
Lambda integrase-like, catalytic core
(d.163.1.1)
1ouq 1
Erythroid transcription factor GATA-1
(g.39.1.1)
1gat 1
Nuclear receptor
(g.39.1.2)
1r0o 1
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