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
HTH_7
(PF02796.14)
5cy2 5cy1 1zr2 1zr4 2gm4 1gdt 15
GntR
(PF00392.20)
5d4r 1hw2 1h9t 4egy 4h0e 5d4s 10
Phage_integrase
(PF00589.21)
5crx 1nzb 1ouq 1q3u 8
UDG
(PF03167.18)
4z47 5ff8 3ufj 3
HTH_1
(PF00126.26)
4ihs 4iht 10
PAX
(PF00292.17)
1mdm 1k78 3
Bac_DnaA_C
(PF08299.10)
1j1v 3pvp 2
HTH_Tnp_Tc3_1
(PF11427.7)
1tc3 1u78 2
BpuJI_N
(PF11564.7)
2vla 5hlt 2
RAG1
(PF12940.6)
5zdz 6cij 2
Homeobox
(PF00046.28)
2ld5 1
GATA
(PF00320.26)
2gat 1
MarR
(PF01047.21)
1z9c 1
FUR
(PF01475.18)
4rb3 1
HTH_Tnp_Mu_1
(PF02316.15)
1g4d 1
FokI_N
(PF02981.14)
1fok 1
GAGA
(PF09237.10)
1yui 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 - 2019

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