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
LacI
(PF00356.20)
2pud 2bjc 2pue 2kei 1vpw 1rzr 1wet 2puf 2puc 2pua 3oqm 3oqn 3oqo 2kek 2kej 2pug 2pub 2pe5 1qqb 1qqa 1pnr 1l1m 1osl 1cjg 1bdi 1bdh 1jfs 1qp4 1jft 1qpz 1jh9 1qp7 1qp0 1lcc 1lcd 43
HTH_8
(PF02954.18)
5e3o 5dtd 5e3l 5e3m 5e3n 5ds9 4fth 3jrc 3jrd 3jre 3jrh 3jri 3jrb 3jra 3iv5 3jr9 31
TetR_N
(PF00440.22)
5hbu 4gcl 3lsr 5k58 5ua1 4l62 4pxi 5dy0 4gct 5gpc 4i6z 5fmp 1jt0 40
Sigma70_r4
(PF04545.15)
5vi8 5vi5 6c04 1ku7 6b6h 5tw1 3n97 4xln 4xls 1rio 4xlp 14
TFIIB
(PF00382.18)
5iy6 5iy8 5iy9 5iyc 5iyd 1d3u 4v1o 4v1n 1c9b 9
HTH_3
(PF01381.21)
1lmb 3u3w 3cro 1per 1rio 1rpe 2or1 1lli 16
Zn_clus
(PF00172.17)
2erg 2ere 1hwt 3coq 1qp9 1f4s 2er8 1f5e 15
mTERF
(PF02536.13)
3n7q 3n6s 3mvb 5crj 3mva 5cky 5co0 5crk 9
Pou
(PF00157.16)
5wc9 1hf0 1cqt 1oct 1au7 3l1p 8
Fe_dep_repress
(PF01325.18)
2isz 2it0 1u8r 1f5t 1ddn 24
HTH_Crp_2
(PF13545.5)
5x6d 4i2o 3mzh 3e6c 5x6e 16
Myb_DNA-binding
(PF00249.30)
1msf 1ign 4gfb 1h89 5
TrmB
(PF01978.18)
5bpd 5bpi 5box 10
HTH_19
(PF12844.6)
4jqd 4jcx 4jcy 8
Peptidase_S48
(PF03574.14)
4hri 4j01 4yrv 7
Rap1-DNA-bind
(PF09197.9)
1ign 4gfb 3ukg 4
MarR
(PF01047.21)
5yi2 5yi3 10
GntR
(PF00392.20)
4p9u 1hw2 5
LexA_DNA_bind
(PF01726.15)
3jsp 3jso 4
HNF-1_N
(PF04814.12)
1ic8 2h8r 4
RHD_DNA_bind
(PF00554.21)
2v2t 5u01 2
Topoisom_I
(PF01028.19)
2h7g 2h7f 2
ARID
(PF01388.20)
1kqq 2oeh 2
zf-CXXC
(PF02008.19)
5w9s 4hp3 2
Sigma54_DBD
(PF04552.12)
2o8k 5ui5 2
Phage_integrase
(PF00589.21)
5jk0 4
HTH_17
(PF12728.6)
6ama 3
zf-C2H2
(PF00096.25)
5k5l 2
HTH_1
(PF00126.26)
4iht 2
Forkhead
(PF00250.17)
2a07 2
P53
(PF00870.17)
4ibu 2
Rep_3
(PF01051.20)
2z9o 2
CUT
(PF02376.14)
2d5v 2
Phage_CII
(PF05269.10)
1zs4 2
KorB
(PF08535.9)
1r71 2
Spo0A_C
(PF08769.10)
1lq1 2
HTH_Tnp_Mu_2
(PF09039.10)
4fcy 2
MqsA_antitoxin
(PF15731.4)
3o9x 2
KORA
(PF16509.4)
5clv 2
Telomere_res
(PF16684.4)
2v6e 2
HLH
(PF00010.25)
1a0a 1
GATA
(PF00320.26)
7gat 1
Trp_repressor
(PF01371.18)
1rcs 1
FUR
(PF01475.18)
4rb3 1
MethyltransfD12
(PF02086.14)
1yfj 1
TFIIF_beta
(PF02270.14)
5fmf 1
HTH_7
(PF02796.14)
2gm4 1
STAT_bind
(PF02864.14)
1bf5 1
HTH_Tnp_Tc5
(PF03221.15)
1hlv 1
Put_DNA-bind_N
(PF06971.12)
3ikt 1
Recombinase
(PF07508.12)
4kis 1
Bac_DnaA_C
(PF08299.10)
3pvv 1
Cdc6_C
(PF09079.10)
2v1u 1
BrkDBD
(PF09607.9)
2glo 1
CRISPR_Cas2
(PF09827.8)
5xvp 1
BpuJI_N
(PF11564.7)
5hlt 1
MarR_2
(PF12802.6)
4fx4 1
Myb_DNA-bind_6
(PF13921.5)
2kdz 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
© NPIDB team 2003 - 2019

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