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
Homeodomain
(PF00046.31)
1ahd 1akh 1apl 1au7 1b72 1b8i 1cqt 1fjl 1gt0 1hdd 1hf0 1ic8 1ig7 1jgg 1k61 1le8 1lfu 1mnm 1nk2 1oct 1puf 1yrn 2d5v 2h1k 2hdd 2hos 2hot 2lkx 2me6 2r5y 2r5z 3a01 3cmy 3d1n 3hdd 3l1p 3lnq 3rkq 4cyc 4j19 4rdu 4s0h 4uus 4xic 4xid 5edn 5eea 5ef6 5eg0 5flv 5hod 5jlw 5jlx 5lty 5lux 5no6 5wc9 5z6z 5zfw 5zfy 5zfz 5zjq 5zjr 5zjs 6a8r 6e8c 6es2 6es3 6m3d 6ryd 6ryi 6ryl 6u81 6u82 6wc2 9ant 131
RAG1
(PF12940.9)
5zdz 5ze0 5ze1 5ze2 6cik 6cil 6cim 6dbq 6dbr 6dbt 6dbu 6dbv 6dbw 6oem 6oen 6oeo 6oep 6oeq 6oer 26
HTH_7
(PF02796.17)
1hcr 1ijw 1jj6 1jj8 1jko 1jkp 1jkq 1jkr 2r0q 12
Telomere_res
(PF16684.7)
4dwp 4e0g 4e0j 4e0p 4e0y 4e0z 4e10 4f41 4f43 9
Phage_integrase
(PF00589.24)
1ouq 1p7d 1pvp 1pvq 1z19 1z1b 1z1g 2a3v 13
Myb_DNA-binding
(PF00249.33)
1iv6 1w0t 1w0u 3sjm 6j4r 6j5b 11
MerR_1
(PF13411.8)
4wls 4wlw 5d8c 6jgw 6jni 6jyw 11
Histone
(PF00125.26)
5gtc 5x0y 6iy2 6m3v 6nj9 6xjd 7
Flp_C
(PF05202.14)
1m6x 1p4e 8
BEN
(PF10523.11)
4ix7 4x0g 4
IRF
(PF00605.19)
1t2k 2o6g 3
Ets
(PF00178.24)
3jtg 4mhg 2
MarR
(PF01047.24)
5hlh 6q2b 2
NDC10_II
(PF16787.7)
3t79 4
EBV-NA1
(PF02905.16)
6pw2 2
IBD
(PF10416.11)
1pp8 2
zf-C4
(PF00105.20)
3g6t 1
PAX
(PF00292.20)
1k78 1
TFIIB
(PF00382.21)
5n9g 1
DNA_topoisoIV
(PF00521.22)
4z2e 1
DM
(PF00751.20)
4yj0 1
Mob_Pre
(PF01076.21)
4lvm 1
PhdYeFM_antitox
(PF02604.21)
4zm2 1
CENP-B_N
(PF04218.15)
1hlv 1
Sigma54_DBD
(PF04552.15)
2o9l 1
RNA_pol_Rpb1_1
(PF04997.14)
6n4c 1
YqaJ
(PF09588.12)
3slp 1
DUF3591
(PF12157.10)
5fur 1
C_LFY_FLO
(PF17538.4)
4bhk 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 1nk3 1oct 1puf 1yrn 2hdd 3hdd 9ant 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 - 2021

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