Interaction mode
Mode:  H-Bb S-Bb S-Mj L-Bb L-Mj 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), β-strand(s) (S) with DNA backbone atoms (Bb), β-strand(s) (S) 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
LAGLIDADG_1
(PF00961.21)
1bp7 1g9y 1g9z 1m5x 1mow 1n3e 1n3f 1p8k 1t9i 1t9j 1u0c 1u0d 2ex5 2fld 2i3p 2i3q 2qoj 2vbj 2vbl 2vbn 2vbo 3e54 3eh8 3fd2 3ko2 3qqy 3r7p 4aab 4aad 4aae 4aaf 4aag 4aqu 4aqx 4efj 4lox 4lq0 4yhx 4yis 4yit 4z1x 4z1z 4z20 5a72 5a74 5a77 5a78 5e5o 5e5s 5e63 5e67 5esp 6bce 6bcf 6bcg 6bch 6bci 6bcn 6bct 6bd0 6bda 6bdb 6fb1 6fb2 6fb5 6fb6 6fb7 6fb8 6fb9 182
IMS_C
(PF11799.10)
1t3n 2dpi 3gv7 3jaa 3mr2 3mr3 4dl2 4dl3 4dl7 4ecr 4ecu 4ecw 4ed6 4f4w 4j9k 4j9l 4j9m 4j9n 4j9o 4j9p 4j9q 4j9s 4o3n 4o3o 4o3p 4o3q 4rnm 4rnn 4rno 4yr2 5dg7 5dg8 5dg9 5dga 5dgb 5dqg 5dqh 5ewe 5f9n 5kfb 5kfc 5kfd 5kfe 5kff 5kfg 5kfh 5kfn 5kfo 5kfp 5kfr 5kft 5kfu 5kfv 5kfy 5kg5 5kg6 5l1j 5l1l 6mp3 6mq8 6mxo 6pl8 6plc 6ui2 64
LAGLIDADG_3
(PF14528.8)
1mow 2vs7 2vs8 4d6n 4d6o 4un7 4un8 4un9 4una 4unb 4unc 4ut0 5a0w 5ak9 5akf 5akm 5akn 5o6g 5o6i 50
MBD
(PF01429.21)
3vxv 3vxx 3vyb 3vyq 5bt2 6c1a 6c1t 6c1u 6c1v 6c2f 6cc8 6ccg 6cnp 6cnq 6ogk 22
MH1
(PF03165.18)
1mhd 1ozj 3kmp 3qsv 5mez 5mf0 5nm9 5x6m 6fzs 6fzt 6h3r 6tbz 6zmn 19
Endonuc-EcoRV
(PF09233.13)
1az0 1b97 1bgb 1bsu 1eo3 1eon 1rv5 1sx8 2b0d 2b0e 5hlk 12
NUDIX_4
(PF14815.8)
1rrq 1rrs 1vrl 4yoq 4yph 4ypr 6q0c 6u7t 9
T_Ag_DNA_bind
(PF02217.18)
2ntc 3qfq 4fb3 4fgn 4gdf 9
RHD_DNA_bind
(PF00554.24)
1owr 1vkx 2as5 3qrf 5u01 6
LAGLIDADG_2
(PF03161.15)
1r7m 3c0w 3c0x 3ool 5a0m 5
MazE_antitoxin
(PF04014.20)
2mru 3zvk 5l6l 6ifm 11
PPV_E1_C
(PF00519.19)
1ksx 1ksy 6
Zn_ribbon_recom
(PF13408.8)
4kis 6dnw 4
B3
(PF02362.23)
5z00 6fas 3
Topoisom_I_N
(PF02919.17)
1seu 1t8i 2
Arc
(PF03869.16)
1bdt 1par 2
LytTR
(PF04397.17)
4xqq 4xyq 2
HTH_56
(PF18662.3)
5vfx 2
AP2
(PF00847.22)
1gcc 1
GCM
(PF03615.17)
1odh 1
Hom_end
(PF05204.16)
1lwt 1
CcdA
(PF07362.14)
2h3c 1
AFT
(PF08731.13)
4lmg 1
Arm-DNA-bind_1
(PF09003.12)
1z1g 1
Endonuc-MspI
(PF09208.12)
1yfi 1
Cas9_C
(PF18525.3)
6joo 1
RE_BsaWI
(PF18643.3)
5dwa 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 EcoRV
(c.52.1.2)
1az0 1b97 1bgb 1bua 1eo3 1eo4 1eon 1eoo 1rv5 1rva 1rvb 1rvc 1stx 1suz 1sx8 2b0d 2b0e 23
Group I mobile intron endonuclease
(d.95.2.1)
1bp7 1g9y 1g9z 1m5x 1mow 1n3e 1n3f 1p8k 1r7m 1t9i 1t9j 1u0c 1u0d 37
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
(e.15.1.1)
1rrj 1seu 1t8i 3
Arc/Mnt-like phage repressors
(a.43.1.1)
1bdt 1par 2
Rel/Dorsal transcription factors, DNA-binding domain
(b.2.5.3)
1owr 1vkx 3
Trafficking protein A-like
(a.43.1.8)
2bsq 2h1o 4
Intein endonuclease
(d.95.2.2)
1lwt 1
SMAD MH1 domain
(d.164.1.1)
1ozj 1
Restriction endonuclease HincII
(c.52.1.19)
1xhu 1
Restriction endonuclease MspI
(c.52.1.23)
1yfi 1
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