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)
4dto 4dtn 4dtm 4dtr 4dts 4dtu 3sq4 4dtx 4du1 5vu7 4du3 4dtj 3uiq 5vu9 3sun 3suo 3sup 3suq 3tab 3tae 3taf 4dtp 5iud 4khs 5vu6 4e3s 4fji 4j2a 4j2b 4j2d 5omv 4m3t 4m3r 4ki6 4j2e 4k8x 4k8z 5gnq 4khn 4khq 4ki4 4khu 4i9q 4m3y 4fk4 4fj5 5omq 4fj7 4fj9 4fjg 4fjh 4fjj 4fjk 4fjl 4fjm 4fjn 4m3z 4fjx 4fk0 4fk2 4khw 3cq8 3nci 2dy4 3ndk 3ne6 3ngi 3nhg 2dtu 3qei 3qep 3qer 3qes 3qet 3qev 3qew 3qex 3nae 3lzj 3cfr 3cfp 2p5o 2p5g 2ozs 2ozm 2oyq 3kd1 3kd5 3l8b 3lzi 3qnn 3sq2 3rmb 3rmc 3rwu 3s9h 3scx 3si6 3sjj 3snn 3spy 3spz 3sq0 3sq1 3rma 3qno 1q9y 1ig9 3lds 1q9x 123
RVT_thumb
(PF06817.13)
5j2p 5txl 5txm 5txn 1t05 5txo 5txp 5j2m 5xn1 5xn2 4r5p 3kle 3jyt 3jsm 3v81 3v6d 5xn0 3v4i 3klf 5i42 3klg 5j2n 5hlf 28
RHD_dimer
(PF16179.4)
3gut 1pzu 2o93 1a3q 1owr 2v2t 1gji 1le5 5u01 1nfk 1ram 2o61 1vkx 2i9t 31
RNA_pol_Rpb1_5
(PF04998.16)
4by7 5vvs 4a93 5iyc 4a3c 5iy8 4a3d 2vum 6bjs 4v1m 6alh 5oqj 6alg 6alf 14
RNA_pol_Rpb1_1
(PF04997.11)
4xls 5oqj 4xlp 5m5x 4a93 5tw1 4xlq 5fz5 6bzo 5fmf 5voi 5vi8 13
DNA_pol_B
(PF00136.20)
4m3u 4m41 2p5g 2dtu 2dy4 2p5o 3rma 3taf 4du4 14
RVT_connect
(PF06815.12)
5hlf 5i3u 5hro 5hp1 3v81 5txn 5txo 9
XPG_I
(PF00867.17)
5t9j 5v09 5v07 3qe9 5uzv 3q8l 8
RNA_pol_Rpb2_1
(PF04563.14)
6b6h 5oik 6asx 6c04 6bjs 4a93 6
RNA_pol_Rpb2_2
(PF04561.13)
4a93 6asx 6c04 6bjs 6b6h 5
DNA_pol_B_thumb
(PF14791.5)
4ymn 4z6d 4nln 4tur 4mf8 5
RNase_H
(PF00075.23)
5xn2 5xn1 5xn0 2hmi 5
RNA_pol_Rpb2_3
(PF04565.15)
5w65 5w66 5vi5 5w5y 4
RbpA
(PF13397.5)
6bzo 5vi8 5vi5 5tw1 4
IMS
(PF00817.19)
1n48 4tqs 2w7o 3
MutS_I
(PF01624.19)
3thy 3thz 1nne 3
PDDEXK_1
(PF12705.6)
4cej 4ceh 4cei 3
Toprim
(PF01751.21)
3foe 3fof 4
UvrD_C
(PF13361.5)
5ld2 4c2t 3
Thioredoxin
(PF00085.19)
2ajq 1t8e 2
Histone
(PF00125.23)
1u35 5x0x 2
TFIIB
(PF00382.18)
5fz5 5fyw 2
MCM
(PF00493.22)
5v8f 5udb 2
RNA_pol_Rpb2_6
(PF00562.27)
5oa1 5w64 2
CBFD_NFYB_HMF
(PF00808.22)
4wzs 1jfi 2
DNA_ligase_ZBD
(PF03119.15)
2owo 4glx 2
TFIIA
(PF03153.12)
5iy6 5iya 2
ResIII
(PF04851.14)
5iy7 5iy6 2
H2TH
(PF06831.13)
2f5n 2f5o 2
C2-set_2
(PF08205.11)
4oi7 4oi8 2
IMS_HHH
(PF11798.7)
3gim 3pw4 2
HHH_6
(PF14579.5)
5fkw 4iqj 2
DNA_ligase_A_M
(PF01068.20)
2q2u 4
Vir_act_alpha_C
(PF10400.8)
5x11 4
NikR_C
(PF08753.10)
2hzv 3
RCC1
(PF00415.17)
3mvd 2
Transposase_1
(PF01359.17)
4u7b 2
HTH_Tnp_Mu_1
(PF02316.15)
4fcy 2
RVT_1
(PF00078.26)
2hmi 1
DNA_methylase
(PF00145.16)
3pta 1
Metallophos
(PF00149.27)
4tug 1
Resolvase
(PF00239.20)
5cy2 1
GATA
(PF00320.26)
4hc9 1
TBP
(PF00352.20)
5oqj 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
RNase_T
(PF00929.23)
5m1s 1
Topoisom_I
(PF01028.19)
1tl8 1
TFIIE_alpha
(PF02002.16)
5fz5 1
MethyltransfD12
(PF02086.14)
1yf3 1
Ku
(PF02735.15)
1jey 1
PCNA_C
(PF02747.14)
3k4x 1
DNA_pol3_beta_2
(PF02767.15)
5m1s 1
Ku_N
(PF03731.14)
1jey 1
Rad4
(PF03835.14)
2qsh 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
Polyoma_lg_T_C
(PF06431.10)
4gdf 1
PriCT_1
(PF08708.10)
3vw4 1
VRR_NUC
(PF08774.10)
5y7g 1
ParB
(PF08775.9)
2ntz 1
BTD
(PF09270.9)
5eg6 1
Mu-transpos_C
(PF09299.10)
4fcy 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
PHD_4
(PF16866.4)
6asb 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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