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
zf-C4
(PF00105.17)
3cbb 3e00 4nqa 1ynw 4iqr 4cn2 3g97 4cn5 3g9i 3g9m 3g9o 3g9p 4cn3 3m9e 3g99 3fyl 3g6q 3g6t 3g6u 3g8u 3g8x 1by4 1r4r 5e6c 5e6b 5e6a 5e69 45
Homeobox
(PF00046.28)
5flv 2r5z 4cyc 1puf 1hdd 2xsd 3hdd 1k61 3a01 5hod 2hot 9ant 1cqt 4uus 1du0 4s0h 4rbo 2hdd 2hos 2d5v 25
Ets
(PF00178.21)
1dux 4iri 3ri4 3mfk 1pue 1awc 4bqa 2nny 4lg0 3wu1 1k6o 1k78 4l0z 1k7a 4l0y 18
TetR_N
(PF00440.22)
4jl3 5k58 4pxi 4l62 5hbu 4gct 4gcl 4gck 2yvh 1jt0 29
Myb_DNA-binding
(PF00249.30)
1h89 1h88 1vfc 3zqc 1msf 3ukg 1mse 5eyb 16
HLH
(PF00010.25)
1a0a 1nlw 4zpk 5sy7 1an4 1mdy 1am9 1an2 11
GerE
(PF00196.18)
1l3l 5vxn 1je8 1zg5 1zlk 1zg1 5w43 22
Histone
(PF00125.23)
3w96 3x1u 5xm1 3w98 3azm 4z5t 6
Pou
(PF00157.16)
1e3o 3d1n 1o4x 1gt0 1hf0 7
HTH_27
(PF13463.5)
5kk1 5k5r 5k5q 5k5o 10
RNA_pol_Rpb1_1
(PF04997.11)
6asx 6alh 6alg 6alf 4
KORA
(PF16509.4)
2w7n 5cm3 5clv 10
MatP
(PF06303.11)
4d8j 3veb 3vea 6
Homeobox_KN
(PF05920.10)
5bng 4xrm 5eg0 5
Phage_integrase
(PF00589.21)
1q3v 1ouq 1z1g 4
IMS_HHH
(PF11798.7)
1n48 4fbu 4tqs 4
HTH_18
(PF12833.6)
3w6v 1bl0 1d5y 4
Topo_C_assoc
(PF14370.5)
2b9s 1a36 1ej9 3
Trp_repressor
(PF01371.18)
1trr 1tro 12
HTH_5
(PF01022.19)
4on0 4omy 8
LacI
(PF00356.20)
3oqo 1rzr 3
PPV_E2_C
(PF00511.16)
2ayb 1jj4 3
E2F_TDP
(PF02319.19)
1cf7 4yo2 3
Phage_int_SAM_1
(PF02899.16)
1p7d 1z1b 3
bZIP_1
(PF00170.20)
1s9k 5t01 2
CUT
(PF02376.14)
2o4a 2o49 2
RAG1
(PF12940.6)
6cim 6cil 2
HTH_IclR
(PF09339.9)
2xro 4
Arg_repressor
(PF01316.20)
3fhz 3
Ftsk_gamma
(PF09397.9)
2ve9 3
IRF
(PF00605.16)
1if1 2
FUR
(PF01475.18)
4rb2 2
z-alpha
(PF02295.16)
4lb5 2
RepA_N
(PF06970.10)
5kbj 2
KorB
(PF08535.9)
1r71 2
HTH_Tnp_Mu_2
(PF09039.10)
4fcy 2
DBD_Tnp_Hermes
(PF10683.8)
4d1q 2
Phage_int_SAM_4
(PF13495.5)
2a3v 2
Myb_DNA-bind_5
(PF13873.5)
5cqq 2
P22_Cro
(PF14549.5)
3qws 2
zf-C2H2
(PF00096.25)
5k5i 1
SRF-TF
(PF00319.17)
1mnm 1
TFIIB
(PF00382.18)
6eu0 1
HSF_DNA-bind
(PF00447.16)
5d5v 1
Trans_reg_C
(PF00486.27)
4kfc 1
DM
(PF00751.17)
4yj0 1
TEA
(PF01285.17)
5gzb 1
HIN
(PF02760.14)
4jbm 1
HTH_8
(PF02954.18)
3jri 1
Peptidase_S48
(PF03574.14)
4j01 1
Penicillinase_R
(PF03965.15)
2d45 1
Sigma54_DBD
(PF04552.12)
5ui5 1
HPD
(PF05044.11)
1xpx 1
Polyoma_lg_T_C
(PF06431.10)
4gdf 1
Put_DNA-bind_N
(PF06971.12)
3ikt 1
GcrA
(PF07750.10)
5z7i 1
Exc
(PF07825.10)
2og0 1
Sigma70_r4_2
(PF08281.11)
2h27 1
Spo0A_C
(PF08769.10)
1lq1 1
ParB
(PF08775.9)
3vwb 1
MerR_1
(PF13411.5)
5c8e 1
NDC10_II
(PF16787.4)
3sqi 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 1oct 1o4x 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 2qhb 1mse 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)
2pe5 1lcc 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
© NPIDB team 2003 - 2019

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