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
(PF00961.18)
4aab 4aqu 3eh8 2vbo 4aqx 4efj 4lox 4lq0 4aag 4aad 3r7p 3fd2 3qqy 3ko2 4aae 4aaf 4yhx 4z20 5a74 5e5s 5a77 5a78 5e5o 5e63 5e67 5esp 4yis 4yit 4z1x 4z1z 2vbn 1n3f 1g9y 1mow 1bp7 1t9i 1t9j 1n3e 1u0c 2ex5 1g9z 1p8k 1m5x 2vbj 2vbl 2i3q 2qoj 2i3p 111
LAGLIDADG_3
(PF14528.5)
5akm 2vs7 4d6n 5ak9 2vs8 5o6i 5o6g 1mow 4un8 4un9 4una 4unc 5a0w 5akn 5akf 4un7 4ut0 37
Endonuc-EcoRV
(PF09233.10)
1eoo 2b0d 5f8a 1az0 1b97 1rv5 1bgb 1rva 1rvb 14
MH1
(PF03165.15)
1ozj 5x6m 5nm9 3kmp 5mez 3qsv 5mf0 9
T_Ag_DNA_bind
(PF02217.15)
2ntc 3qfq 4gdf 4fb3 4fgn 9
RHD_DNA_bind
(PF00554.21)
5u01 2as5 1vkx 1owr 5
MazE_antitoxin
(PF04014.17)
2mru 5l6l 3zvk 9
LAGLIDADG_2
(PF03161.12)
3c0x 5a0m 1r7m 3
PPV_E1_C
(PF00519.16)
1ksx 1ksy 8
LytTR
(PF04397.14)
4xyq 4xqq 2
CcdA
(PF07362.11)
2h3a 2h3c 2
AP2
(PF00847.19)
1gcc 1
MBD
(PF01429.18)
6c1v 1
BamHI
(PF02923.14)
2bam 1
GCM
(PF03615.14)
1odh 1
Hom_end
(PF05204.13)
1lwt 1
Arm-DNA-bind_1
(PF09003.9)
1z1g 1
Endonuc-MspI
(PF09208.9)
1yfi 1
IMS_C
(PF11799.7)
1t3n 1
Zn_ribbon_recom
(PF13408.5)
4kis 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
© NPIDB team 2003 - 2019

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