Interaction mode
Mode:  H-Bb L-Bb L-Mn 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), 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
RNase_H
(PF00075.23)
1r0a 4r5p 5j2p 3klf 3kle 3kjv 3jsm 1t03 5j2n 5j2m 1rtd 12
TFIIF_beta
(PF02270.14)
5iya 5iy7 5iy6 5iyc 5iyb 5iy8 6
DNA_pol_A
(PF00476.19)
5c53 4x0p 5c52 3
UvrD-helicase
(PF00580.20)
4ceh 4cei 4cej 3
RNA_pol_Rpb1_5
(PF04998.16)
4a3i 3po2 4by1 3
DNA_pol_B
(PF00136.20)
3rmb 4ki6 2
UDG
(PF03167.18)
4z7z 3ufj 2
BTD
(PF09270.9)
3brd 3iag 2
YqaJ
(PF09588.9)
3sm4 4wuz 2
BHD_1
(PF10403.8)
2qsg 2qsh 2
HHH_5
(PF14520.5)
2owo 4glx 2
BEN
(PF10523.8)
4x0g 2
HMG_box
(PF00505.18)
3nm9 1
Phage_integrase
(PF00589.21)
2a3v 1
Histone_HNS
(PF00816.20)
2lev 1
Toprim
(PF01751.21)
3ksb 1
Herpes_alk_exo
(PF01771.16)
3pov 1
N6_Mtase
(PF02384.15)
4xqk 1
5_3_exonuc_N
(PF02739.15)
2ihn 1
Mab-21
(PF03281.13)
4o6a 1
KilA-N
(PF04383.12)
4ux5 1
RNaseH_C
(PF09293.9)
2ihn 1
UvrD_C
(PF13361.5)
4c2u 1
AAA_22
(PF13401.5)
2qby 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
DNA repair glycosylase, 2 C-terminal domains
(a.96.1.3)
1ebm 1hu0 1n3a 1n3c 1yql 1yqm 2i5w 2nob 3cw7 9
Eukaryotic DNA topoisomerase I, catalytic core
(d.163.1.2)
1lpq 1r49 1t8i 3
Nucleosome core histones
(a.22.1.1)
1kx4 3b6f 2
T4 endonuclease V
(a.18.1.1)
1vas 1
HMG-box
(a.21.1.1)
1hry 1
Mismatch glycosylase
(a.96.1.2)
1rrq 1
Lambda integrase-like, catalytic core
(d.163.1.1)
1ma7 1
DNA-binding protein LAG-1 (CSL)
(b.42.7.1)
3brd 1
ATP-dependent DNA ligase DNA-binding domain
(a.235.1.1)
1x9n 1
© NPIDB team 2003 - 2017

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