Interaction mode
Mode:  H-Bb H-Mj L-Bb L-Mn 
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 minor groove of DNA (Mn).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
Homeobox
(PF00046.28)
1yrn 3d1n 3hdd 3l1p 3lnq 3rkq 4cyc 3a01 2r5z 2d5v 2h1k 2hdd 2hos 2hot 2lkx 2me6 5wc9 2r5y 4j19 5lty 5lux 6es2 6es3 5hod 5flv 5eg0 4rdu 4uus 4xid 5edn 5eea 9ant 1le8 1fjl 1akh 1gt0 1hdd 1hf0 1mnm 1oct 1nk3 1nk2 1ig7 1jgg 1lfu 1cqt 1b72 1apl 1au7 1puf 1b8i 83
HTH_7
(PF02796.14)
2r0q 1hcr 1jj8 1jko 1jkp 1jkq 1jkr 1ijw 11
Telomere_res
(PF16684.4)
4e0y 4dwp 4e0g 4e0j 4e0p 4f43 4f41 4e0z 8
RAG1
(PF12940.6)
6cim 5ze2 6cik 6cil 5ze1 5ze0 5zdz 10
Phage_integrase
(PF00589.21)
1pvp 1z19 1p7d 2a3v 1z1g 10
Myb_DNA-binding
(PF00249.30)
1w0t 3sjm 1w0u 1iv6 7
Flp_C
(PF05202.11)
1m6x 1p4e 8
BEN
(PF10523.8)
4x0g 4ix7 4
IRF
(PF00605.16)
1t2k 2o6g 3
Histone
(PF00125.23)
5x0y 5gtc 2
Ets
(PF00178.21)
3jtg 4mhg 2
IBD
(PF10416.8)
1pp8 1pp7 2
MogR_DNAbind
(PF12181.7)
3fdq 2
PAX
(PF00292.17)
1k78 1
GntR
(PF00392.20)
5d4s 1
MarR
(PF01047.21)
5hlh 1
CENP-B_N
(PF04218.12)
1hlv 1
Sigma54_DBD
(PF04552.12)
2o9l 1
YqaJ
(PF09588.9)
3slp 1
DUF3591
(PF12157.7)
5fur 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
Homeodomain
(a.4.1.1)
1akh 1apl 1au7 1b72 1b8i 1cqt 1fjl 1gt0 1hdd 1hf0 1ic8 1ig7 1jgg 1k61 1le8 1mnm 1oct 1puf 1yrn 2hdd 3hdd 9ant 1nk3 33
Lambda integrase-like, catalytic core
(d.163.1.1)
1kbu 1m6x 1ouq 1p4e 1p7d 1pvp 1pvq 1pvr 1xns 1xo0 1z1b 1z1g 4crx 5crx 23
Recombinase DNA-binding domain
(a.4.1.2)
1hcr 1ijw 1jj6 1jj8 1jko 1jkp 1jkq 1jkr 1u78 1zr2 2gm4 11
Nucleosome core histones
(a.22.1.1)
1kx3 1kx5 2nzd 2pyo 3b6f 3b6g 9
SRF-like
(d.88.1.1)
1hbx 1k6o 1mnm 1n6j 1srs 1tqe 10
Paired domain
(a.4.1.5)
1k78 1mdm 6pax 5
DNA repair glycosylase, 2 C-terminal domains
(a.96.1.3)
1fn7 1m3q 2
39 kda initiator binding protein, IBP39, N-terminal domain
(a.4.5.44)
1pp7 1pp8 3
Centromere-binding
(a.4.1.7)
1hlv 1
Cell cycle transcription factor e2f-dp
(a.4.5.17)
1cf7 1
Trp repressor, TrpR
(a.4.12.1)
1trr 1
© NPIDB team 2003 - 2019

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