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
HTH_3
(PF01381.21)
4x4c 4x4b 4z5d 4iwr 4x4d 4x4h 4x4i 4yg1 4z5c 4x4g 4x4e 4x4f 2r1j 3s8q 3jxd 3jxc 3jxb 3clc 3ufd 4ivz 3zkc 53
NDT80_PhoG
(PF05224.11)
2euv 1mnn 2evh 2etw 2evg 2evj 2euw 2evi 2eux 2evf 2euz 11
Pou
(PF00157.16)
1au7 1cqt 2xsd 3
Forkhead
(PF00250.17)
3l2c 4lg0 5dui 3
Flp_N
(PF03930.13)
1p4e 1m6x 4
P53
(PF00870.17)
3q05 4mzr 3
MarR
(PF01047.21)
4aij 3q5f 3
zf-C4
(PF00105.17)
1r4i 1r0n 2
MarR_2
(PF12802.6)
4lln 4lll 2
HSF_DNA-bind
(PF00447.16)
5d8l 4
FUR
(PF01475.18)
4mtd 4
Trans_reg_C
(PF00486.27)
4s05 2
HxlR
(PF01638.16)
4hqe 2
RTP
(PF02334.15)
1f4k 2
STAT_bind
(PF02864.14)
5d39 2
Histone
(PF00125.23)
2fj7 1
Ets
(PF00178.21)
3wtw 1
GATA
(PF00320.26)
3dfv 1
BRCT
(PF00533.25)
2k7f 1
Rep_3
(PF01051.20)
2nra 1
E2F_TDP
(PF02319.19)
4yo2 1
FokI_C
(PF02980.15)
1fok 1
Endonuc-BglII
(PF09195.10)
2p0j 1
MerR_1
(PF13411.5)
5c8e 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 - 2017

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