Interaction mode
Mode:  H-Bb H-Mj 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), loop(s) (L) with DNA backbone atoms (Bb).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
Homeodomain
(PF00046.31)
1akh 1cqt 1du0 1hdd 1ic8 1k61 1puf 1yrn 2hdd 2hos 2hot 2xsd 3a01 3hdd 4rbo 4s0h 4uus 5edn 5flv 5hod 5zjr 5zjs 6u81 6u82 9ant 31
zf-C4
(PF00105.20)
1by4 1ynw 3e00 3fyl 3g6q 3g6t 3g6u 3g8u 3g8x 3g97 3g99 3g9i 3g9m 3g9o 3g9p 4cn2 4iqr 4nqa 5e69 5e6a 5e6b 5e6c 6xwh 33
Integrase_H2C2
(PF17921.3)
3l2r 3l2u 3l2v 3l2w 3os0 3os1 3os2 3oye 3oyh 3oyj 4bac 4bdz 4be1 4e7j 4e7k 4e7l 4ikf 5frn 5mmb 5uop 20
Ets
(PF00178.24)
1k6o 1k78 1k7a 1pue 2nny 2stt 3mfk 3ri4 3wts 3wtu 3wtv 3wtx 4bqa 4iri 4l0y 4l0z 4l18 4uuv 5zmc 30
RNA_pol_Rpb1_1
(PF04997.14)
2o5j 2ppb 4wqs 5m5x 5zx2 6c6s 6c6t 6dv9 6dve 6k4y 6kon 6kop 6koq 6rh3 6ri9 6tye 6tyf 6tyg 18
zf-H2C2_2
(PF13465.8)
1ubd 5eh2 5k5h 5kkq 5t00 5t0u 5und 5v3j 5vmx 5vmz 5yef 5yeg 5yeh 6df8 6df9 25
TetR_N
(PF00440.25)
1jt0 2yvh 4gck 4gcl 4gct 4jl3 4l62 4pxi 5hbu 5k58 5k7z 5vl9 6c31 6o6p 39
HLH
(PF00010.28)
1a0a 1am9 1an4 1mdy 1nkp 1nlw 2ql2 4atk 4h10 4zpk 5nj8 5sy7 5v0l 6od3 25
HTH_3
(PF01381.24)
4x4b 4x4c 4x4d 4x4e 4x4f 4x4g 4x4h 4x4i 4yg4 4yg7 5jub 6fix 6lb3 13
Histone
(PF00125.26)
3azi 3azm 3w96 3w98 4z5t 5cpk 5xm1 5z3l 6r91 6ven 7crq 14
GerE
(PF00196.21)
1je8 1l3l 1zg1 1zg5 1zlk 5vxn 5w43 6ide 25
Myb_DNA-binding
(PF00249.33)
1h88 1h89 1vfc 3zqc 5eyb 6j4r 6j5b 6kks 20
Sigma70_r4
(PF04545.18)
4xlr 6omf 6psv 6wmt 6wmu 6wr8 7c17 7khi 8
Pou
(PF00157.19)
1e3o 1gt0 1hf0 1o4x 3d1n 5wc9 6ht5 10
TFIIB
(PF00382.21)
1c9b 6cnb 6cnc 6cnd 6cnf 6eu0 6f42 8
IMS_HHH
(PF11798.10)
1n48 2au0 4fbu 4g3i 4tqs 6l84 8
HTH_27
(PF13463.8)
5k1y 5k5o 5k5q 5k5r 5kk1 22
Homeobox_KN
(PF05920.13)
4xrm 5bng 5eg0 6fqp 6fqq 10
MerR_1
(PF13411.8)
4wls 5c8e 5d8c 5e01 5i44 7
Phage_int_SAM_1
(PF02899.19)
1p7d 1z19 1z1b 1z1g 10
DBD_Tnp_Hermes
(PF10683.11)
4d1q 6dww 6dwy 6dwz 5
HTH_18
(PF12833.9)
1bl0 1d5y 1xs9 3w6v 5
HTH_Crp_2
(PF13545.8)
1cgp 6b6h 6pb5 6pb6 5
Myb_DNA-bind_6
(PF13921.8)
1mse 1msf 3osg 5eyb 4
Topo_C_assoc
(PF14370.8)
1a35 1a36 1ej9 2b9s 4
MatP
(PF06303.14)
3vea 3veb 4d8j 9
HTH_48
(PF17906.3)
3hot 4r79 4u7b 5
TEA
(PF01285.20)
5gzb 5nnx 5no6 4
Put_DNA-bind_N
(PF06971.15)
3ikt 3il2 3ket 4
Sigma70_r4_2
(PF08281.14)
2h27 5zx2 6jhe 4
HTH_ParB
(PF17762.3)
6s6h 6t1f 6y93 4
LacI
(PF00356.23)
1osl 1rzr 7ce1 3
H2TH
(PF06831.16)
3sar 3sav 3sbj 3
CENP-T_C
(PF15511.8)
5z3l 6m4d 6xjd 3
Trp_repressor
(PF01371.21)
1tro 1trr 12
HTH_5
(PF01022.22)
4omy 4on0 8
KORA
(PF16509.7)
5clv 5cm3 6
IRF
(PF00605.19)
1if1 2irf 5
Recombinase
(PF07508.15)
4kis 6dnw 4
bZIP_1
(PF00170.23)
1s9k 5t01 3
DNA_topoisoIV
(PF00521.22)
3foe 3fof 3
E2F_TDP
(PF02319.22)
1cf7 4yo2 3
Exc
(PF07825.13)
2og0 6p0t 2
RAG1
(PF12940.9)
6cil 6cim 2
ORC4_C
(PF14629.8)
6wgc 6wgg 2
FtsK_gamma
(PF09397.12)
2ve9 6
Penicillinase_R
(PF03965.18)
2d45 4
HTH_IclR
(PF09339.12)
2xro 4
Phage_int_SAM_4
(PF13495.8)
2a3v 4
Arg_repressor
(PF01316.23)
3fhz 3
PPV_E2_C
(PF00511.19)
2ayb 2
HTH_Tnp_Mu_1
(PF02316.18)
4fcy 2
Polyoma_lg_T_C
(PF06431.13)
4gdf 2
RepA_N
(PF06970.13)
5kbj 2
KorB
(PF08535.12)
1r71 2
Spo0A_C
(PF08769.13)
1lq1 2
HTH_Tnp_Mu_2
(PF09039.13)
4fcy 2
Myb_DNA-bind_5
(PF13873.8)
5cqq 2
Bac_DNA_binding
(PF00216.23)
6o8q 1
Forkhead
(PF00250.20)
6ncm 1
SRF-TF
(PF00319.20)
1mnm 1
Trans_reg_C
(PF00486.30)
4kfc 1
Phage_integrase
(PF00589.24)
1z1g 1
DM
(PF00751.20)
4yj0 1
5_3_exonuc
(PF01367.22)
5hnk 1
FUR
(PF01475.21)
4rb2 1
z-alpha
(PF02295.19)
3irq 1
RTP
(PF02334.18)
2dpu 1
ERCC4
(PF02732.17)
4p0r 1
HTH_8
(PF02954.21)
3jri 1
Peptidase_S48
(PF03574.17)
4j00 1
Sigma54_DBD
(PF04552.15)
5ui5 1
HPD
(PF05044.14)
1xpx 1
Phage_antitermQ
(PF06530.14)
6p1a 1
GcrA
(PF07750.13)
5z7i 1
ParB
(PF08775.12)
3vwb 1
HTH_37
(PF13744.8)
6lty 1
HHH_8
(PF14716.8)
4klm 1
NDC10_II
(PF16787.7)
3sqi 1
Cep3
(PF16846.7)
6gys 1
FANC_SAP
(PF18081.3)
4r89 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
lambda integrase-like, N-terminal domain
(a.60.9.1)
1crx 1drg 1f44 1kbu 1ma7 1nzb 1ouq 1pvp 1pvq 1pvr 1q3u 1q3v 1xns 1xo0 2crx 2hof 2hoi 3crx 4crx 5crx 48
Homeodomain
(a.4.1.1)
1akh 1cqt 1du0 1e3o 1hdd 1ic8 1k61 1puf 1xpx 1yrn 2hdd 2r5y 2r5z 3hdd 9ant 17
CAP C-terminal domain-like
(a.4.5.4)
1cgp 1j59 1lb2 1o3q 1o3r 1o3s 1o3t 1run 1ruo 1zrc 1zrf 15
ets domain
(a.4.5.21)
1awc 1bc8 1dux 1k6o 1k78 1k7a 1pue 2stw 9
POU-specific domain
(a.35.1.1)
1au7 1cqt 1e3o 1gt0 1hf0 1o4x 1oct 9
DNA-binding N-terminal domain of transcription activators
(a.6.1.3)
1r8d 1r8e 3d6y 3d6z 3d70 3d71 7
Leucine zipper domain
(h.1.3.1)
1gtw 1gu4 1gu5 1h88 1h8a 1hjb 9
Myb/SANT domain
(a.4.1.3)
1h88 1h89 1h8a 1mse 2qhb 8
HLH, helix-loop-helix DNA-binding domain
(a.38.1.1)
1a0a 1am9 1an4 1mdy 1nlw 10
Nuclear receptor
(g.39.1.2)
1by4 1dsz 1glu 1r4r 1ynw 6
Interferon regulatory factor
(a.4.5.23)
1if1 1t2k 2irf 2o6g 9
Iron-dependent repressor protein
(a.4.5.24)
1ddn 1f5t 2isz 2it0 11
GerE-like (LuxR/UhpA family of transcriptional regulators)
(a.4.6.2)
1je8 1l3l 1zg1 1zg5 15
Lambda integrase-like, catalytic core
(d.163.1.1)
1flo 1m6x 1p4e 1z1g 7
AraC type transcriptional activator
(a.4.1.8)
1bl0 1d5y 3
Replication terminator protein (RTP)
(a.4.5.7)
2dpu 2efw 3
GalR/LacI-like bacterial regulator
(a.35.1.5)
1lcc 2pe5 3
Trp repressor, TrpR
(a.4.12.1)
1tro 1trr 7
Viral DNA-binding domain
(d.58.8.1)
1jj4 2ayb 3
Recombinase DNA-binding domain
(a.4.1.2)
1zr2 1
Methylated DNA-protein cysteine methyltransferase, C-terminal domain
(a.4.2.1)
1t39 1
Cell cycle transcription factor e2f-dp
(a.4.5.17)
1cf7 1
Excisionase-like
(a.6.1.7)
2og0 1
Nucleosome core histones
(a.22.1.1)
1kx4 1
Phage repressors
(a.35.1.2)
6cro 1
Transcription factor IIB (TFIIB), core domain
(a.74.1.2)
1c9b 2
SRF-like
(d.88.1.1)
1mnm 1
Eukaryotic DNA topoisomerase I, catalytic core
(d.163.1.2)
1ej9 1
Classic zinc finger, C2H2
(g.37.1.1)
1a1i 1
Penicillinase repressor
(a.4.5.39)
2d45 4
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