Interaction mode
Mode:  H-Bb H-Mn L-Bb 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), helix(es) (H) with the minor groove of DNA (Mn), loop(s) (L) with DNA backbone atoms (Bb).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
DNA_pol_lambd_f
(PF10391.11)
1xsp 2bcq 2bcr 2bcs 2bcu 2pfn 2pfo 2pfp 3c5g 3hw8 3hwt 3mdc 3upq 4p4o 4p4p 4x5v 4xa5 5cwr 5iij 5iil 5iim 5iin 22
DNA_ligase_A_N
(PF04675.16)
6p09 6p0b 6p0c 6p0d 6p0e 6q1v 6
RNase_H
(PF00075.26)
4htu 4hue 4hug 6an8 6anq 5
SNF2-rel_dom
(PF00176.25)
6iy2 6jyl 6kw3 6kw5 4
DNA_pol_B_thumb
(PF14791.8)
1bpz 1huo 2bpg 3pml 4
Mab-21
(PF03281.16)
4ley 4lez 4o6a 5
HMG_box
(PF00505.21)
5jgh 6cg0 6edb 3
IMS
(PF00817.22)
1zet 2dpi 2fll 3
Topoisom_I
(PF01028.22)
1rr8 1sc7 1seu 3
Sulf_coat_C
(PF12193.10)
3j9x 5w7g 77
Metallophos
(PF00149.30)
3dsc 3dsd 2
RVT_thumb
(PF06817.16)
3kk3 6kdo 2
HMG_box_2
(PF09011.12)
4nod 4
SASP
(PF00269.22)
2z3x 3
UvrD_C
(PF13361.8)
2is2 2
rve
(PF00665.28)
6voy 1
RNase_T
(PF00929.26)
4fzx 1
DNA_binding_1
(PF01035.22)
4enm 1
DNA_ligase_A_M
(PF01068.23)
6ras 1
Y1_Tnp
(PF01797.18)
2a6o 1
Cas_Cas1
(PF01867.18)
5wfe 1
CarD_CdnL_TRCF
(PF02559.18)
6vw0 1
RNA_pol_A_CTD
(PF03118.17)
6vvs 1
RNA_pol_Rpb1_5
(PF04998.19)
4wqs 1
DNA_alkylation
(PF08713.13)
5clc 1
TOPRIM_C
(PF16898.7)
3qx3 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
Eukaryotic DNA topoisomerase I, catalytic core
(d.163.1.2)
1a35 1a36 1ej9 1k4t 1sc7 5
HMG-box
(a.21.1.1)
1ckt 1qrv 2
DNA repair glycosylase, 2 C-terminal domains
(a.96.1.3)
1lwv 1
© NPIDB team 2003 - 2021

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