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 3kjv 4r5p 3v81 5txp 3jsm 5j2m 5j2n 1rtd 1t03 5txo 3kle 5txn 5j2p 14
Toprim
(PF01751.21)
5iwm 2xcs 4plb 5iwi 3ksb 2xcr 4bul 12
TFIIF_beta
(PF02270.14)
5iyc 5iyb 5iy8 5iy7 5iy6 5iya 6
DNA_pol_A
(PF00476.19)
4x0p 5c52 5c53 3
UvrD-helicase
(PF00580.20)
4cei 4cej 4ceh 3
RNA_pol_Rpb1_5
(PF04998.16)
4by1 4a3i 3po2 3
DNA_pol_B
(PF00136.20)
4ki6 3rmb 2
BTD
(PF09270.9)
3brd 3iag 2
YqaJ
(PF09588.9)
4wuz 3sm4 2
BHD_1
(PF10403.8)
2qsh 2qsg 2
HHH_5
(PF14520.5)
4glx 2owo 2
BEN
(PF10523.8)
4x0g 2
HMG_box
(PF00505.18)
3nm9 1
Histone_HNS
(PF00816.20)
2lev 1
Topoisom_I
(PF01028.19)
1t8i 1
Herpes_alk_exo
(PF01771.16)
3pov 1
5_3_exonuc_N
(PF02739.15)
2ihn 1
UDG
(PF03167.18)
3ufj 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 - 2019

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