Interaction mode
Mode:  L-Bb 
Description: Conserved protein-DNA contacts are provided by loop(s) (L) with DNA backbone atoms (Bb).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
DNA_pol_B_exo1
(PF03104.18)
3qep 3qer 3qes 3qet 3qev 3spy 3qew 3qex 3qnn 3qno 3uiq 3qei 4dts 4dtm 3nae 3nci 3ndk 3ne6 4dtn 3ngi 3nhg 4dto 4du1 4dtp 4dtr 4dtu 3taf 4dtj 3sun 3sq4 3sq2 3sq1 4dtx 3rwu 3s9h 3scx 3si6 3sjj 3snn 3sq0 3suo 3rmc 3tab 3tae 3rma 3suq 3sup 3rmb 3spz 2dtu 4ki4 4khw 4khu 4khs 4khq 4khn 4k8z 4k8x 4j2e 4j2d 4j2b 2oyq 4ki6 4m3r 1ig9 5iud 1q9x 1q9y 4m3z 4m3y 4i9q 2dy4 4m3t 2ozm 2ozs 2p5g 4fjh 4fjg 4fj9 3kd1 3kd5 4fj7 4fj5 4e3s 4du3 3l8b 3lds 3lzi 4fji 4fjj 4fjk 4j2a 4fk4 4fk2 4fk0 4fjx 3cfp 3cfr 4fjl 4fjm 4fjn 2p5o 3cq8 3lzj 117
RVT_thumb
(PF06817.13)
3v4i 3v6d 5i42 3v81 1t05 4r5p 3kle 3jyt 3jsm 5hlf 5j2p 5j2n 3klf 3klg 5j2m 20
RHD_dimer
(PF16179.4)
1le5 1a3q 1nfk 1le9 2o61 2o93 2v2t 3gut 2i9t 1vkx 1owr 1pzu 1ram 29
DNA_pol_B
(PF00136.20)
2dy4 2dtu 4m3u 3taf 3rma 2p5g 2p5o 3rmd 4du4 4m41 15
RNA_pol_Rpb1_5
(PF04998.16)
4a93 2o5j 5iy8 5iyc 4by7 2vum 3gtg 7
RNA_pol_Rpb1_1
(PF04997.11)
4xlp 4xlq 4xls 2o5j 5fz5 8
DNA_pol_B_thumb
(PF14791.5)
4tur 4mf8 4z6d 4ymn 4nln 5
RVT_connect
(PF06815.12)
5hro 5i3u 5hlf 5hp1 6
XPG_I
(PF00867.17)
5t9j 3qe9 3q8l 4
IMS
(PF00817.19)
2w7p 1n48 4tqs 3
Topoisom_I
(PF01028.19)
1tl8 1sc7 1rr8 3
PDDEXK_1
(PF12705.6)
4ceh 4cej 4cei 3
Toprim
(PF01751.21)
3fof 3foe 10
UvrD_C
(PF13361.5)
4c2t 5ld2 5
Thioredoxin
(PF00085.19)
1t8e 2ajq 2
Metallophos
(PF00149.27)
4tui 4tug 2
TFIIB
(PF00382.18)
5fyw 5fz5 2
CBFD_NFYB_HMF
(PF00808.22)
4wzs 1jfi 2
MutS_I
(PF01624.19)
3thy 1nne 2
TFIIA
(PF03153.12)
5iy6 5iya 2
ResIII
(PF04851.14)
5iy7 5iy6 2
H2TH
(PF06831.13)
2f5o 2f5n 2
C2-set_2
(PF08205.11)
4oi8 4oi7 2
IMS_HHH
(PF11798.7)
3gim 3pw4 2
HHH_6
(PF14579.5)
5fkw 4iqj 2
NikR_C
(PF08753.10)
2hzv 3
RCC1
(PF00415.17)
3mvd 2
Polyoma_lg_T_C
(PF06431.10)
4gdf 2
RNase_H
(PF00075.23)
2hmi 1
RVT_1
(PF00078.26)
2hmi 1
Histone
(PF00125.23)
1u35 1
DNA_methylase
(PF00145.16)
3pta 1
DNA_topoisoIV
(PF00521.19)
2xkk 1
IN_DBD_C
(PF00552.20)
5ejk 1
UvrD-helicase
(PF00580.20)
2is2 1
PCNA_N
(PF00705.17)
3k4x 1
DNA_pol3_beta
(PF00712.18)
5fkv 1
DNA_ligase_A_M
(PF01068.20)
2q2u 1
TFIIE_alpha
(PF02002.16)
5fz5 1
MethyltransfD12
(PF02086.14)
1yf3 1
Ku
(PF02735.15)
1jey 1
PCNA_C
(PF02747.14)
3k4x 1
DNA_ligase_ZBD
(PF03119.15)
2owo 1
Ku_N
(PF03731.14)
1jey 1
Rad4
(PF03835.14)
2qsh 1
RNA_pol_Rpb2_2
(PF04561.13)
4a93 1
RNA_pol_Rpb2_1
(PF04563.14)
4a93 1
MutS_III
(PF05192.17)
3thz 1
RusA
(PF05866.10)
2h8c 1
Tfb5
(PF06331.11)
5fmf 1
DNA_pol3_alpha
(PF07733.11)
4iqj 1
ParB
(PF08775.9)
2ntz 1
RNA_ligase
(PF09414.9)
2hvr 1
AAA_16
(PF13191.5)
2v1u 1
AAA_22
(PF13401.5)
2qby 1
ERCC3_RAD25_C
(PF16203.4)
5fmf 1
Histone_H2A_C
(PF16211.4)
1aoi 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
DnaQ-like 3'-5' exonuclease
(c.55.3.5)
1ig9 1njy 1njz 1q9x 1q9y 1t8e 1tk0 1tk8 1tkd 1ua1 1x9m 1x9w 1zyq 2dy4 2oyq 2ozm 2ozs 2p5g 2p5o 3cq8 25
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
(b.1.18.1)
1a3q 1le5 1le9 1lei 1nfk 1owr 1pzu 1ram 1svc 1vkx 2i9t 2o61 2o93 2ram 2v2t 29
N-terminal domain of MutM-like DNA repair proteins
(b.113.1.1)
1k3x 1l2b 1r2y 1r2z 2f5q 2f5s 6
Middle domain of MutM-like DNA repair proteins
(a.156.1.2)
1k3w 1k82 2ea0 2f5s 2oq4 8
DNA repair protein MutS, domain I
(d.75.2.1)
1e3m 1ng9 1nne 1oh8 4
Single-strand selective monofunctional uracil-DNA glycosylase SMUG1
(c.18.1.3)
1oe4 1oe5 1oe6 3
Leucine zipper domain
(h.1.3.1)
1hwt 2hap 3
C-terminal, Zn-finger domain of MutM-like DNA repair proteins
(g.39.1.8)
1l2b 2oq4 2
ets domain
(a.4.5.21)
1hbx 2
T4 endonuclease V
(a.18.1.1)
2fcc 2
Nucleosome core histones
(a.22.1.1)
1kx3 1
GalR/LacI-like bacterial regulator
(a.35.1.5)
1jwl 1
Endonuclease III
(a.96.1.1)
1p59 1
Mismatch glycosylase
(a.96.1.2)
1vrl 1
Trp repressor, TrpR
(a.4.12.1)
1co0 1
DNA repair protein MutS, domain III
(a.113.1.1)
1oh8 1
SRF-like
(d.88.1.1)
1srs 1
Classic zinc finger, C2H2
(g.37.1.1)
2gli 1
DNA-binding domains of HMG-I(Y)
(j.10.1.1)
2ezf 1
RecG "wedge" domain
(b.40.4.9)
1gm5 1
Achaeal helicase C-terminal domain
(a.289.1.2)
2p6r 1
© NPIDB team 2003 - 2017

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