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)
1qpz 1qqa 1qqb 1qp7 1wet 1rzr 2bjc 2pe5 3oqm 2pug 2puf 2pue 2pud 2puc 2kek 2kej 3oqn 2kei 3oqo 1qp4 1qp0 1lcc 1cjg 1l1m 1jh9 1jft 1jfs 1efa 1lcd 1osl 1bdh 1pnr 1bdi 43
HTH_8
(PF02954.18)
5e3m 4fth 3jrd 5dtd 3jrc 3jri 3jrh 3jre 3jra 5ds9 5e3l 3iv5 3jr9 5e3o 5e3n 3jrb 31
TetR_N
(PF00440.22)
4l62 5fmp 4gcl 4pxi 4gct 5k58 5dy0 5hbu 1jt0 30
Zn_clus
(PF00172.17)
1qp9 2er8 3coq 1f5e 1f4s 2erg 2ere 1hwt 1d66 16
TFIIB
(PF00382.18)
1c9b 5iyc 5iy9 5iy6 4v1n 1d3u 5iyd 5iy8 4v1o 11
mTERF
(PF02536.13)
5crk 3mva 3mvb 3n7q 3n6s 5crj 5cky 5co0 8
HTH_3
(PF01381.21)
1lmb 1lli 1rio 1rpe 1per 3cro 2or1 14
Sigma70_r4
(PF04545.15)
1ku7 4xln 1rio 4xlp 3n97 4xls 9
Pou
(PF00157.16)
1hf0 1oct 1e3o 3l1p 1cqt 1au7 7
Fe_dep_repress
(PF01325.18)
1u8r 2it0 1f5t 2isz 1ddn 24
Myb_DNA-binding
(PF00249.30)
1ign 1msf 1h89 4gfb 5
TrmB
(PF01978.18)
5bpd 5bpi 5box 10
HTH_19
(PF12844.6)
4jcx 4jcy 4jqd 8
Peptidase_S48
(PF03574.14)
4yrv 4hri 4j01 7
Rap1-DNA-bind
(PF09197.9)
1ign 3ukg 4gfb 4
HTH_Crp_2
(PF13545.5)
3e6c 3mzh 4i2o 4
Crp
(PF00325.19)
5ciz 1cgp 2cgp 3
LexA_DNA_bind
(PF01726.15)
3jso 3jsp 4
HNF-1_N
(PF04814.12)
1ic8 2h8r 4
GntR
(PF00392.20)
1hw2 4p9u 3
Topoisom_I
(PF01028.19)
2h7g 2h7f 2
ARID
(PF01388.20)
2oeh 1kqq 2
HTH_1
(PF00126.26)
4iht 2
Forkhead
(PF00250.17)
2a07 2
P53
(PF00870.17)
4ibu 2
Rep_3
(PF01051.20)
2z9o 2
Trp_repressor
(PF01371.18)
1rcs 2
CUT
(PF02376.14)
2d5v 2
Phage_CII
(PF05269.10)
1zs4 2
Spo0A_C
(PF08769.10)
1lq1 2
MqsA_antitoxin
(PF15731.4)
3o9x 2
KORA
(PF16509.4)
5clv 2
Telomere_res
(PF16684.4)
2v6e 2
HLH
(PF00010.25)
1a0a 1
Homeobox
(PF00046.28)
2h8r 1
RHD_DNA_bind
(PF00554.21)
2v2t 1
FUR
(PF01475.18)
4rb3 1
zf-CXXC
(PF02008.19)
4hp3 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
Sigma54_DBD
(PF04552.12)
2o8k 1
Put_DNA-bind_N
(PF06971.12)
3ikt 1
Recombinase
(PF07508.12)
4kis 1
Bac_DnaA_C
(PF08299.10)
3pvv 1
BpuJI_N
(PF11564.7)
5hlt 1
MarR_2
(PF12802.6)
4fx4 1
HTH_AsnC-type
(PF13404.5)
2e1c 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 - 2017

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