Interaction mode
Mode:  H-Bb S-Bb L-Bb L-Mj L-Mn 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), β-strand(s) (S) with DNA backbone atoms (Bb), 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
Fapy_DNA_glyco
(PF01149.26)
2f5n 2f5o 3sar 3sas 3sat 3sau 3sav 3saw 3sbj 3u6c 3u6d 3u6e 3u6o 3u6p 3u6q 3u6s 4g4o 17
Exo_endo_phos
(PF03372.25)
1dew 1dnk 2voa 3g00 3g0r 4b5f 4b5j 4gz2 5wn0 5wn1 6fk4 6fk5 6w4t 16
SAD_SRA
(PF02182.19)
2zkd 2zo0 2zo1 3clz 3fde 4pw5 4pw7 4qen 4qeo 4qep 6a5n 16
Endonuc-PvuII
(PF09225.12)
1eyu 1f0o 1pvi 2pvi 3pvi 9
XPA_C
(PF05181.14)
5a3d 5g32 5g33 5g34 5lcm 5
DNA_topoisoIV
(PF00521.22)
3raf 4z3o 4z4q 4z53 6
RPOL_N
(PF14700.8)
1cez 1qln 2pi4 2pi5 4
RE_Eco29kI
(PF09517.12)
3mx4 3nic 8
Cas_Cas1
(PF01867.18)
5ds6 5wfe 4
RecA
(PF00154.23)
3cmt 7jy7 3
Bac_DNA_binding
(PF00216.23)
2np2 5wfe 3
RHD_DNA_bind
(PF00554.24)
1a02 1pzu 3
Histone
(PF00125.26)
6m44 6om3 2
MutS_I
(PF01624.22)
3thw 3thx 2
SeqA
(PF03925.15)
1j3e 1lrr 2
RAG1
(PF12940.9)
6dbw 6v0v 2
Cas9_PI
(PF16595.7)
5b2t 5fq5 2
MethyltransfD12
(PF02086.17)
2g1p 2
RQC
(PF09382.12)
3aaf 2
DNA_pol_B
(PF00136.23)
3k5m 1
Helicase_C
(PF00271.33)
6kw4 1
DNA_pol_A
(PF00476.22)
1x9s 1
rve
(PF00665.28)
4bac 1
Topoisom_I
(PF01028.22)
2b9s 1
RNase_HII
(PF01351.20)
3o3g 1
N6_Mtase
(PF02384.18)
4xqk 1
DNA_pol3_alpha
(PF07733.14)
3e0d 1
Endonuc-EcoRV
(PF09233.13)
5hlk 1
TaqI_C
(PF12950.9)
2np6 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
N-terminal domain of MutM-like DNA repair proteins
(b.113.1.1)
1nnj 1pji 1pjj 1pm5 1tdz 1xc8 6
Restriction endonuclease PvuII
(c.52.1.6)
1eyu 1f0o 1pvi 6
Rel/Dorsal transcription factors, DNA-binding domain
(b.2.5.3)
1pzu 2
3-methyladenine DNA glycosylase (AAG, ANPG, MPG)
(b.46.1.2)
1f6o 1
Restriction endonuclease EcoRV
(c.52.1.2)
4rve 1
Restriction endonuclease BamHI
(c.52.1.3)
2bam 1
Restriction endonuclease BglI
(c.52.1.4)
1dmu 1
DNA-binding domain from NDT80
(b.2.5.7)
2euz 1
© NPIDB team 2003 - 2021

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