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
GntR
(PF00392.20)
4egy 4h0e 1h9t 5d4r 5d4s 1hw2 10
HTH_7
(PF02796.14)
1zr4 1gdt 1zr2 2gm4 9
Phage_integrase
(PF00589.21)
1q3u 5crx 1ouq 1nzb 8
UDG
(PF03167.18)
5hf7 5ff8 3ufj 3
Bac_DnaA_C
(PF08299.10)
3pvv 1j1v 3pvp 3
HTH_1
(PF00126.26)
4iht 4ihs 6
PAX
(PF00292.17)
1mdm 1k78 3
GAGA
(PF09237.10)
1yuj 1yui 2
HTH_Tnp_Tc3_1
(PF11427.7)
1u78 1tc3 2
MarR_2
(PF12802.6)
4lll 2
Homeobox
(PF00046.28)
2ld5 1
GATA
(PF00320.26)
2gat 1
FUR
(PF01475.18)
4rb3 1
zf-CXXC
(PF02008.19)
4z3c 1
HTH_Tnp_Mu_1
(PF02316.15)
1g4d 1
FokI_N
(PF02981.14)
1fok 1
BrkDBD
(PF09607.9)
2glo 1
BpuJI_N
(PF11564.7)
2vla 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 - 2017

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