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
(PF00075.26)
1r0a 1rtd 1t03 3jsm 3kjv 3kle 3klf 3v81 4r5p 5j2m 5j2n 5j2p 5txn 5txo 5txp 6amo 6an8 6avm 6avt 6otz 6p1i 6p1x 6p2g 6uir 6uit 6ujx 6ujy 6uk0 32
Toprim
(PF01751.24)
2xcr 2xcs 2xct 3ksa 3ksb 3rad 4bul 4i3h 4kpe 4kpf 4plb 4z2c 4z2e 5cdp 5eix 5iwi 5iwm 6fm4 6fqv 6qtk 6qtp 6qx2 6z1a 49
Histone
(PF00125.26)
6iro 6iy3 6j99 6kiu 6kiv 6kiw 6kix 6kiz 6kw5 6ne3 6o96 6om3 6t7a 6t7c 7crp 7crq 7crr 20
Mab-21
(PF03281.16)
4k96 4k98 4k99 4ley 4o6a 5xzg 6y5d 7c0m 8
TFIIF_beta
(PF02270.17)
5iy6 5iy7 5iy8 5iya 5iyb 5iyc 6
RNA_pol_Rpb1_5
(PF04998.19)
3po2 4a3g 4a3i 4bxx 4by1 6uq3 6
DNA_pol_A
(PF00476.22)
4x0p 4ztu 4ztz 5c52 5c53 5
DNA_pol_B
(PF00136.23)
2vwj 6s1m 6tny 6tnz 4
BHD_1
(PF10403.11)
2qsg 2qsh 6cfi 6ubf 4
HMG_box
(PF00505.21)
3nm9 6oem 6oen 4
RVT_1
(PF00078.29)
6or7 6otz 6p1i 3
UvrD-helicase
(PF00580.23)
4ceh 4cei 4cej 3
HhH-GPD
(PF00730.27)
3cvs 3cvt 4ea5 3
UDG
(PF03167.21)
2rba 3ufj 3
Exo_endo_phos
(PF03372.25)
3ga6 5dg0 2
RVT_thumb
(PF06817.16)
6ik9 6kdm 2
YqaJ
(PF09588.12)
3sm4 4wuz 2
HHH_5
(PF14520.8)
2owo 4glx 2
DNA_alkylation
(PF08713.13)
5vhv 2
BEN
(PF10523.11)
4x0g 2
SNF2-rel_dom
(PF00176.25)
5z3l 1
Helicase_C
(PF00271.33)
6o8e 1
TFIIB
(PF00382.21)
4roe 1
Histone_HNS
(PF00816.23)
2lev 1
Topoisom_I
(PF01028.22)
1t8i 1
GIY-YIG
(PF01541.26)
6sei 1
EVE
(PF01878.20)
5j3e 1
RuvC
(PF02075.19)
4ld0 1
Ku
(PF02735.18)
5y3r 1
Pyr_excise
(PF03013.16)
1vas 1
RNA_pol_A_CTD
(PF03118.17)
5vi8 1
Adenine_glyco
(PF03352.15)
2ofi 1
TCR
(PF03638.17)
5fd3 1
KilA-N
(PF04383.15)
4ux5 1
DNA_ligase_A_N
(PF04675.16)
1x9n 1
H2TH
(PF06831.16)
1r2y 1
RNaseH_C
(PF09293.12)
2ihn 1
DUF3591
(PF12157.10)
6mzm 1
RAG1
(PF12940.9)
6dbx 1
AAA_16
(PF13191.8)
2v1u 1
UvrD_C
(PF13361.8)
4c2u 1
AAA_22
(PF13401.8)
2qby 1
AAA_23
(PF13476.8)
5f3w 1
DNA_pol_B_thumb
(PF14791.8)
3mgh 1
Myb_DNA-bind_7
(PF15963.7)
6f40 1
ERCC3_RAD25_C
(PF16203.7)
6ro4 1
DNA_pol3_finger
(PF17657.3)
3f2d 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 - 2021

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