Interaction mode
Mode:  H-Bb H-Mj L-Bb L-Mj 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 major groove of DNA (Mj), loop(s) (L) with the minor groove of DNA (Mn).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
Phage_integrase
(PF00589.24)
1kbu 1nzb 1ouq 1pvr 1q3u 1xo0 1z19 1z1g 3c28 4crx 5crx 13
Exo_endo_phos
(PF03372.25)
1de8 5dff 5dfh 5dfj 5wn3 6bos 6bou 6p93 6p94 6w0q 6w43 11
RAG1
(PF12940.9)
5zdz 6cij 6dbi 6dbl 6dbo 6dbr 6oer 6oet 9
UDG
(PF03167.21)
3ufj 4z47 5ff8 5hf7 5jxy 6u16 6u17 8
HTH_7
(PF02796.17)
1gdt 1zr2 1zr4 2gm4 5cy1 5cy2 15
Homeodomain
(PF00046.31)
1hf0 2ld5 5z6z 5zjt 6e8c 7
DNA_topoisoIV
(PF00521.22)
2xct 3ltn 4z2c 4z2d 5
HhH-GPD
(PF00730.27)
1diz 1n3c 4ypr 5kn9 5
BpuJI_N
(PF11564.10)
2vla 5hlt 5hnf 5hnh 4
Bac_DnaA_C
(PF08299.13)
1j1v 3pvp 3pvv 5
HTH_1
(PF00126.29)
4ihs 4iht 10
Fe_dep_repress
(PF01325.21)
2isz 2it0 4
Myb_DNA-binding
(PF00249.33)
1ign 4gfb 3
PAX
(PF00292.20)
1k78 1mdm 3
GntR
(PF00392.23)
1h9t 1hw2 3
DNA_methylase
(PF00145.19)
1dct 6w8w 2
Zn_clus
(PF00172.20)
6e33 6o19 2
HTH_3
(PF01381.24)
1per 2or1 2
zf-CXXC
(PF02008.22)
4hp3 4z3c 2
GAGA
(PF09237.13)
1yui 1yuj 2
HTH_Tnp_Tc3_1
(PF11427.10)
1tc3 1u78 2
MarR_2
(PF12802.9)
4lll 2
GATA
(PF00320.29)
2gat 1
LacI
(PF00356.23)
1lcc 1
DNA_pol_A
(PF00476.22)
6dsy 1
MarR
(PF01047.24)
1z9c 1
FUR
(PF01475.21)
4rb3 1
CUT
(PF02376.17)
2d5v 1
FokI_N
(PF02981.17)
1fok 1
BrkDBD
(PF09607.12)
2glo 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
Recombinase DNA-binding domain
(a.4.1.2)
1gdt 1tc3 1u78 1zr4 8
Paired domain
(a.4.1.5)
1k78 1mdm 3
GntR-like transcriptional regulators
(a.4.5.6)
1h9t 1hw2 3
Lambda integrase-like, catalytic core
(d.163.1.1)
1nzb 1q3u 2
Centromere-binding
(a.4.1.7)
1hlv 1
Restriction endonuclease FokI, N-terminal (recognition) domain
(a.4.5.12)
1fok 1
MarR-like transcriptional regulators
(a.4.5.28)
1z9c 1
Rel/Dorsal transcription factors, DNA-binding domain
(b.2.5.3)
1ooa 1
Classic zinc finger, C2H2
(g.37.1.1)
1yui 1
Zn2/Cys6 DNA-binding domain
(g.38.1.1)
1f5e 1
© NPIDB team 2003 - 2021

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