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)
3suo 3uiq 3tae 3tab 3sq1 3sq0 4m3z 4m3y 3suq 3taf 3sq4 3sun 3sup 4khq 4fk0 4fjx 4fjn 4fjm 4fjl 4fjk 4fjj 4fji 4fk2 4fk4 4khu 4khn 4k8z 4k8x 4j2e 4j2d 4j2b 4j2a 4i9q 4fjh 4fjg 4dtr 4dtp 4dto 4dtn 4dtm 4dtj 4ki6 4m3r 4dts 4dtu 4dtx 4fj9 4fj7 4khw 4khs 4e3s 4ki4 4du3 4du1 4m3t 1ig9 5omq 3cfp 3cfr 3cq8 5vu9 5iud 3kd1 3kd5 5gnq 3l8b 3lds 5omv 2p5o 1q9x 1q9y 2dtu 2dy4 5vu7 5vu6 3sq2 2oyq 2ozm 2ozs 2p5g 3lzi 3spz 3qew 3qex 3qnn 3qno 3rma 3rmb 3rmc 3rwu 3s9h 3scx 3si6 3sjj 3snn 3spy 3qev 3ndk 3lzj 3nae 3nci 3ne6 3ngi 3nhg 4fj5 3qei 3qes 3qer 3qet 3qep 123
RVT_thumb
(PF06817.13)
5xn2 3v81 5txo 5txp 5hlf 5txl 5txm 5txn 3kle 1t05 3v4i 5xn0 3jsm 5j2p 3jyt 3klg 3klf 5i42 5j2m 5j2n 3v6d 5xn1 4r5p 28
RNA_pol_Rpb1_5
(PF04998.16)
5vvs 5iyc 2vum 5iy8 6alf 4a93 6exv 6eu1 6eu0 4by7 4a3d 6bjs 6alh 5oqj 6alg 4a3c 4v1m 17
RHD_dimer
(PF16179.4)
5u01 2o93 1nfk 1owr 1a3q 1le5 1gji 1ram 2o61 3gut 2i9t 2v2t 1vkx 1pzu 31
RNA_pol_Rpb1_1
(PF04997.11)
5m5x 5voi 5vi8 4xlp 4xlq 4xls 4a93 5oqj 5tw1 5fmf 5fz5 6bzo 13
DNA_pol_B
(PF00136.20)
2p5o 2p5g 2dtu 3taf 2dy4 3rma 4m41 4m3u 4du4 14
RVT_connect
(PF06815.12)
5txo 5txn 3v81 5hp1 5i3u 5hro 5hlf 9
RNA_pol_Rpb2_1
(PF04563.14)
6b6h 6asx 6bjs 6c04 5oik 6f42 4a93 7
XPG_I
(PF00867.17)
5uzv 5t9j 5v07 3q8l 5v09 3qe9 8
RNA_pol_Rpb2_2
(PF04561.13)
6c04 6bjs 6b6h 4a93 6asx 6f42 6
RNA_pol_Rpb2_3
(PF04565.15)
5vi5 5w5y 5w66 5w65 6eu0 5
DNA_pol_B_thumb
(PF14791.5)
4ymn 4tur 4mf8 4nln 4z6d 5
RNase_H
(PF00075.23)
5xn1 5xn2 5xn0 2hmi 5
RbpA
(PF13397.5)
6bzo 5tw1 5vi8 5vi5 4
MCM
(PF00493.22)
5v8f 6f0l 5udb 4
TFIIB
(PF00382.18)
5fz5 6f42 5fyw 3
IMS
(PF00817.19)
2w7o 1n48 4tqs 3
MutS_I
(PF01624.19)
1nne 3thz 3thy 3
PDDEXK_1
(PF12705.6)
4cei 4ceh 4cej 3
Toprim
(PF01751.21)
3fof 3foe 4
UvrD_C
(PF13361.5)
4c2t 5ld2 3
Thioredoxin
(PF00085.19)
1t8e 2ajq 2
Histone
(PF00125.23)
1u35 5x0x 2
RNA_pol_Rpb2_6
(PF00562.27)
5w64 5oa1 2
CBFD_NFYB_HMF
(PF00808.22)
1jfi 4wzs 2
DNA_ligase_ZBD
(PF03119.15)
2owo 4glx 2
TFIIA
(PF03153.12)
5iya 5iy6 2
ResIII
(PF04851.14)
5iy7 5iy6 2
H2TH
(PF06831.13)
2f5o 2f5n 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
MCM_OB
(PF17207.2)
6f0l 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
RrnaAD
(PF00398.19)
6erq 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_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
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
HMG_box_2
(PF09011.9)
6cg0 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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