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)
3uiq 3sq2 3taf 4m3y 3sq1 4m3t 3spz 3spy 3snn 3sjj 4m3z 3sq4 3sq0 3tab 3tae 3suq 3sup 3suo 3sun 4m3r 4ki6 4fjh 4fji 4fjj 4fjk 4fjl 4fjm 4fjn 4fjx 4fk0 4fk2 4fk4 4k8z 4k8x 4i9q 4j2e 4j2d 4j2a 4fjg 4fj9 4fj7 4ki4 4khw 4khu 4khs 4khq 4dtj 4dtm 4dtn 4dto 4dtp 4dtr 4dts 4dtu 4dtx 4khn 4e3s 4fj5 4j2b 1ig9 3cfr 3cq8 5iud 3kd1 3kd5 5gnq 3l8b 3lds 3lzi 3cfp 5omq 2p5o 1q9x 1q9y 4du1 2dtu 5vu9 5vu7 5vu6 4du3 2ozm 2ozs 2p5g 3lzj 3si6 3qex 3rmd 3qnn 3qno 3rmb 3rmc 3rwu 3s9h 3scx 3qew 3qev 3nci 3ndk 3ne6 3ngi 3nhg 3qei 3nae 3qep 3qer 3qes 3qet 5omv 121
RVT_thumb
(PF06817.13)
5txo 5txn 5txm 5txl 5j2m 5j2p 5txp 5j2n 3klf 5xn1 1t05 3v6d 3v81 4r5p 5xn2 5xn0 3klg 3jsm 3jyt 5i42 5hlf 3kle 33
RNA_pol_Rpb1_5
(PF04998.16)
5vvs 5oqj 6eu0 5iyc 2o5j 6eu1 6exv 2vum 6bjs 5iy8 4by7 6alg 6alf 4a93 6alh 15
RHD_dimer
(PF16179.4)
3gut 2v2t 2o61 1le9 5u01 1le5 2o93 1a3q 1nfk 1vkx 1ram 1pzu 1owr 31
RNA_pol_Rpb1_1
(PF04997.11)
5vi5 4xls 4xlq 5tw1 4xlp 5fz5 5vi8 5oqj 6bzo 5voi 10
DNA_pol_B
(PF00136.20)
2p5o 3rmd 3taf 4m41 2p5g 4m3u 2dtu 4du4 10
RVT_connect
(PF06815.12)
5hp1 5hro 5i3u 5hlf 5txo 5txn 3v81 9
RNA_pol_Rpb2_1
(PF04563.14)
6c04 6asx 6bjs 6b6h 6f42 4a93 5oik 7
XPG_I
(PF00867.17)
3q8l 5t9j 5uzv 3qe9 5v07 5v09 7
RNA_pol_Rpb2_2
(PF04561.13)
6asx 4a93 6b6h 6f42 6bjs 6c04 6
RNase_H
(PF00075.23)
5xn1 5xn0 5xn2 2hmi 6
RNA_pol_Rpb2_3
(PF04565.15)
5w5y 5w65 5w66 6eu0 4
RbpA
(PF13397.5)
6bzo 5vi5 5vi8 5tw1 4
DNA_pol_B_thumb
(PF14791.5)
4ymn 4nln 4z6d 4mf8 4
UvrD_C
(PF13361.5)
5ld2 4c2t 2is1 6
MCM
(PF00493.22)
6f0l 5udb 5v8f 4
TFIIB
(PF00382.18)
6f42 5fyw 5fz5 3
IMS
(PF00817.19)
4tqs 2w7p 1n48 3
Topoisom_I
(PF01028.19)
1tl8 1rr8 1sc7 3
PDDEXK_1
(PF12705.6)
4cej 4ceh 4cei 3
Toprim
(PF01751.21)
3foe 3fof 10
Thioredoxin
(PF00085.19)
2ajq 1t8e 2
Histone
(PF00125.23)
1u35 5x0x 2
Metallophos
(PF00149.27)
4tug 4tui 2
RrnaAD
(PF00398.19)
6erq 6erp 2
RNA_pol_Rpb2_6
(PF00562.27)
5w64 5oa1 2
MutS_I
(PF01624.19)
3thy 1nne 2
DNA_ligase_ZBD
(PF03119.15)
2owo 4glx 2
TFIIA
(PF03153.12)
5iya 5iy6 2
ResIII
(PF04851.14)
5iy6 5iy7 2
H2TH
(PF06831.13)
2f5n 2f5o 2
C2-set_2
(PF08205.11)
4oi8 4oi7 2
IMS_HHH
(PF11798.7)
3gim 3pw4 2
HHH_6
(PF14579.5)
4iqj 5fkw 2
Vir_act_alpha_C
(PF10400.8)
5x11 6
NikR_C
(PF08753.10)
2hzv 3
PHD_4
(PF16866.4)
6asb 3
RCC1
(PF00415.17)
3mvd 2
Polyoma_lg_T_C
(PF06431.10)
4gdf 2
VRR_NUC
(PF08774.10)
5y7g 2
MCM_OB
(PF17207.2)
6f0l 2
RVT_1
(PF00078.26)
2hmi 1
DNA_methylase
(PF00145.16)
3pta 1
Resolvase
(PF00239.20)
5cy2 1
TBP
(PF00352.20)
5oqj 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
CBFD_NFYB_HMF
(PF00808.22)
1jfi 1
RNase_T
(PF00929.23)
5m1s 1
TFIIE_alpha
(PF02002.16)
5fz5 1
MethyltransfD12
(PF02086.14)
1yf3 1
PCNA_C
(PF02747.14)
3k4x 1
DNA_pol3_beta_2
(PF02767.15)
5m1s 1
Rad4
(PF03835.14)
2qsh 1
RNA_pol_Rpb5_N
(PF03871.13)
6eu1 1
RNA_pol_I_TF
(PF04090.11)
5oa1 1
MutS_III
(PF05192.17)
3thz 1
TFIIF_alpha
(PF05793.11)
5sva 1
RusA
(PF05866.10)
2h8c 1
Tfb5
(PF06331.11)
5fmf 1
DNA_pol3_alpha
(PF07733.11)
4iqj 1
ParB
(PF08775.9)
2ntz 1
HMG_box_2
(PF09011.9)
6cg0 1
BTD
(PF09270.9)
5eg6 1
RNA_ligase
(PF09414.9)
2hvr 1
Cas_Cas5d
(PF09704.9)
5u07 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 - 2019

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