Interaction mode
Mode:  H-Bb H-Mj S-Bb 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), β-strand(s) (S) with DNA backbone atoms (Bb), 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
zf-H2C2_2
(PF13465.8)
1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l 1aay 1f2i 1g2d 1g2f 1jk1 1jk2 1llm 1p47 1tf3 1zaa 2i13 4r2a 4r2c 4r2e 4r2p 4r2q 4r2r 4x9j 5egb 5eh2 5ei9 5k5i 5k5j 5ke9 5kkq 5kl2 5kl3 5kl4 5kl5 5kl6 5kl7 5t00 5t0u 5und 5v3j 5v3m 5wjq 5yef 5yeg 6b0o 6b0p 6b0r 6ki6 6ml2 6ml3 6ml4 6ml5 6ml6 6ml7 91
P53
(PF00870.20)
2ac0 2ady 2geq 3d0a 3exj 3kmd 3q05 3q06 3qyn 3us0 4guo 4ibu 4mzr 6fj5 25
NDT80_PhoG
(PF05224.14)
1mnn 2etw 2euv 2euw 2eux 2euz 2evf 2evg 2evh 2evi 2evj 11
zf-C4
(PF00105.20)
1r0n 1r0o 1r4i 2a66 2nll 3cbb 3m9e 5krb 5l0m 11
FOXP-CC
(PF16159.7)
4r2e 4r2p 4r2q 4r2r 5kl3 5kl4 5kl5 5kl6 5kl7 9
zf-C2H2
(PF00096.28)
4gzn 4m9v 5yj3 11
MarR
(PF01047.24)
3q5f 4aij 5yi2 7
PadR
(PF03551.16)
5x11 6qfd 6qil 6
Forkhead
(PF00250.20)
3l2c 4lg0 5dui 3
FUR
(PF01475.21)
4mtd 4mte 8
CRISPR_Cas2
(PF09827.11)
5xvn 5xvo 6
HTH_17
(PF12728.9)
6ama 6amk 5
HSF_DNA-bind
(PF00447.19)
5d5v 5d8l 4
DpnI_C
(PF17726.3)
4esj 4kyw 3
BamHI
(PF02923.17)
2bam 3bam 2
Flp_N
(PF03930.16)
1m6x 1p4e 2
MarR_2
(PF12802.9)
4lll 4lln 2
zf-C2H2_11
(PF16622.7)
6e93 6e94 2
Zn-ribbon_8
(PF09723.12)
2i13 3
GntR
(PF00392.23)
6za3 2
Trans_reg_C
(PF00486.30)
4s05 2
Phage_integrase
(PF00589.24)
2a3v 2
HxlR
(PF01638.19)
4hqe 2
RTP
(PF02334.18)
1f4k 2
zf-Di19
(PF05605.14)
2drp 2
Histone
(PF00125.26)
2fj7 1
HTH_1
(PF00126.29)
5xxp 1
Zn_clus
(PF00172.20)
1zme 1
Ets
(PF00178.24)
3wtw 1
GATA
(PF00320.29)
3dfv 1
BRCT
(PF00533.28)
2k7f 1
Rep_3
(PF01051.23)
2nra 1
Endonuclease_NS
(PF01223.25)
6iid 1
ARID
(PF01388.23)
6lqf 1
E2F_TDP
(PF02319.22)
4yo2 1
FokI_C
(PF02980.18)
1fok 1
HVO_2753_ZBP
(PF07754.13)
5v3j 1
Endonuc-BglII
(PF09195.13)
2p0j 1
MerR_1
(PF13411.8)
5c8e 1
HTH_Crp_2
(PF13545.8)
3e6c 1
CENP-T_C
(PF15511.8)
1zbb 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
Restriction endonuclease EcoRI
(c.52.1.1)
1ckq 1eri 1qps 1qrh 1qri 5
Rel/Dorsal transcription factors, DNA-binding domain
(b.2.5.3)
1owr 1s9k 2as5 2o93 5
Restriction endonuclease BglII
(c.52.1.5)
1d2i 1dfm 4
Classic zinc finger, C2H2
(g.37.1.1)
1f2i 2drp 5
Restriction endonuclease FokI, N-terminal (recognition) domain
(a.4.5.12)
1fok 1
lambda integrase-like, N-terminal domain
(a.60.9.1)
1m6x 1
Lambda integrase-like, catalytic core
(d.163.1.1)
1q3v 1
Zinc finger design
(k.12.1.1)
1mey 2
© NPIDB team 2003 - 2021

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