Interaction mode
Mode:  L-Bb 
Description: Conserved protein-DNA contacts are provided by loop(s) (L) with DNA backbone atoms (Bb).
Pfam domains
Export table
Pfam Domain Family PDB entries Number of structures
DNA_pol_B_exo1
(PF03104.21)
1ig9 1q9x 1q9y 2dtu 2dy4 2oyq 2ozm 2ozs 2p5g 2p5o 3cfp 3cfr 3cq8 3kd1 3kd5 3l8b 3lds 3lzi 3lzj 3nae 3nci 3ndk 3ne6 3ngi 3nhg 3qet 3qev 3qew 3qex 3qnn 3qno 3rma 3rmb 3rmc 3rmd 3s9h 3scx 3si6 3sjj 3snn 3spy 3spz 3sq0 3sq1 3sq2 3sq4 3sun 3suo 3sup 3suq 3tab 3tae 3taf 3tag 3uiq 4dtj 4dtm 4dtn 4dto 4dtp 4dtr 4dts 4dtu 4dtx 4du1 4du3 4e3s 4fj5 4fj7 4fj8 4fj9 4fjg 4fjh 4fji 4fjj 4fjk 4fjl 4fjm 4fjn 4fjx 4fk0 4fk2 4fk4 4i9q 4j2a 4j2b 4j2d 4j2e 4k8x 4k8z 4khn 4khq 4khs 4khu 4khw 4khy 4ki4 4ki6 4m3r 4m3t 4m3u 4m3x 4m3y 4m3z 4m41 4m42 4m45 5iud 5omq 5omv 5vu6 5vu7 5vu9 6wya 133
RNA_pol_Rpb1_5
(PF04998.19)
1y77 2vum 3gtg 4a3c 4a3d 4a93 4by7 4v1m 5c4j 5iy7 5iy8 5iyb 5iyc 5oqj 5vvs 5w51 6alf 6alg 6alh 6bjs 6c6t 6c6u 6eu0 6eu1 6exv 6flq 6gml 6h67 6h68 6kf9 6o6c 6oul 6psv 6ri7 6rip 6rrd 6upy 6upz 6uq2 6wr6 6wr8 6wrg 7c97 7khc 7khe 45
RNA_pol_Rpb1_1
(PF04997.14)
2ja8 2o5j 4a93 4wqs 4xlp 4xlq 4xls 5fz5 5oqj 5sva 5tw1 5vi8 5voi 6bzo 6cce 6ccv 6cnb 6cnc 6cuu 6dcf 6flq 6gyk 6h68 6jbq 6jnx 6kj6 6ldi 6m7j 6n60 6n61 6pb5 6pss 6psu 6rie 6vvs 6vvt 6vvv 6vvy 6vw0 6wrd 6wrg 7khe 47
RNA_pol_Rpb2_1
(PF04563.17)
4a3e 4a93 5oik 5uhd 6asx 6b6h 6bjs 6c04 6cnf 6dv9 6dvb 6dvd 6dve 6edt 6ee8 6eec 6eu0 6f42 6flq 6j9e 6kon 6omf 6pb4 6pb6 6pmi 6ri9 6rip 6tye 6tyf 6tyg 6vvx 6vvy 6vvz 6vw0 6wmu 6wr8 7khc 37
Taq-exonuc
(PF09281.12)
3lwm 3m8r 3ojs 3oju 3po4 3py8 3rr7 3rrg 3rtv 3sz2 3t3f 4bwj 4df8 4dfj 4dfm 4dfp 4dle 4dlg 4elu 4elv 5e41 5nkl 5o7t 5oxj 5szt 5ytc 5ytf 5ytg 5z3n 6fbc 6fbd 6fbe 6fbf 6fbh 6fbi 6q4u 6q4v 37
HHH_8
(PF14716.8)
1zqa 1zqb 1zqg 1zqi 1zqn 1zqo 1zqp 1zqt 3rh4 3rji 4kld 4klf 4kls 4pgx 4uaw 5eoz 5hhi 5j0w 5u2r 5v1o 5wo0 6cpq 6cr5 6ctr 6ctx 6e3w 6u2o 7icn 8icc 8icj 9ick 9icn 9icp 9icr 9ics 35
RNA_pol_Rpb2_2
(PF04561.16)
4a3e 4a93 5uhd 6asx 6b6h 6bjs 6c04 6dv9 6dvb 6dvd 6dve 6edt 6ee8 6eec 6f42 6flq 6omf 6pb4 6pb6 6pmi 6pst 6ri9 6rip 6tye 6tyf 6tyg 6vvx 6vvy 6vvz 6vw0 6wmu 6wr8 7khc 33
RHD_dimer
(PF16179.7)
1a3q 1gji 1le5 1le9 1lei 1nfk 1owr 1pzu 1ram 1vkx 2i9t 2o61 2o93 2ram 2v2t 3do7 3gut 5u01 38
RNA_pol_Rpb2_3
(PF04565.18)
1y1w 2ja8 3h3v 5oa1 5vi5 5w5y 5w64 5w65 5w66 6cuu 6ee8 6eec 6eu0 6gml 6oul 6pb6 6tps 6vvz 18
RbpA
(PF13397.8)
5tw1 5vi5 5vi8 6bzo 6cce 6ccv 6dcf 6edt 6ee8 6eec 6m7j 6vvs 6vvt 6vvv 6vvx 6vvy 6vvz 6vw0 18
DNA_pol_B_thumb
(PF14791.8)
3isb 3uxp 4m9h 4mf8 4nln 4tur 4ymn 4z6d 5dbc 5j0q 5u8g 5u8h 5u8i 5v1g 6cua 6e3x 6mr7 6u6b 18
RVT_connect
(PF06815.15)
3v81 5hlf 5hp1 5hro 5i3u 5txn 5txo 5xn0 5xn1 5xn2 6ik9 6kdj 6kdm 6kdn 6kdo 6o9e 24
CENP-T_C
(PF15511.8)
6iro 6iy3 6kiu 6kiv 6kiw 6kix 6kiz 6kw5 6m4d 6nqa 6t7b 6ven 7cro 7crq 17
RNase_H_2
(PF13482.8)
1skr 1sks 1sl2 1t7p 1t8e 1tk0 1tk5 1tk8 1tkd 1x9m 1x9w 1zyq 4ynq 13
IN_DBD_C
(PF00552.23)
5ejk 6put 6puy 6puz 6rwl 6rwm 6rwn 6rwo 6u8q 6v3k 6vdk 6voy 18
XPG_I
(PF00867.20)
1rxw 3q8l 3qe9 4q10 5co8 5t9j 5um9 5uzv 5v07 5v09 5v0a 5v0d 15
RNase_H
(PF00075.26)
2hmi 5xn0 5xn1 5xn2 6ik9 6ika 6kdj 6kdk 6kdm 6kdn 6kdo 20
MutS_I
(PF01624.22)
1e3m 1ng9 1nne 1oh6 1oh8 1wb9 1wbd 3k0s 3thy 9
rve
(PF00665.28)
3jca 6put 6puw 6puy 6puz 6u8q 6v3k 6z2y 11
RVT_thumb
(PF06817.16)
5hlf 5i42 5xn0 5xn1 5xn2 6kdj 6kdk 6kdo 10
MutS_III
(PF05192.20)
1oh8 2o8b 2o8c 2o8d 2o8f 3thw 3thx 3thz 8
Toprim
(PF01751.24)
2xct 3foe 3fof 6rks 6rku 6rkv 6rkw 9
UvrD_C
(PF13361.8)
1w36 4c2t 5ld2 6ppr 6ppu 6sje 6sjf 9
IMS
(PF00817.22)
2w7o 2w7p 4u7c 5w2a 6jul 6jum 6jup 8
H2TH
(PF06831.16)
2f5n 2oq4 3sat 3saw 3u6c 3u6e 3u6p 7
Histone
(PF00125.26)
6m4g 6m4h 6t7a 6t7b 6t7d 6yov 10
MutS_IV
(PF05190.20)
1oh8 2o8b 2o8c 2o8f 3thw 3thx 6
DNA_pol_B
(PF00136.23)
2dtu 2p5g 2p5o 3rma 3rmd 8
Ku_N
(PF03731.17)
1jey 5y3r 6erf 6erg 6erh 8
Ku
(PF02735.18)
1jey 6erg 6erh 6zha 6zhe 7
SET
(PF00856.30)
6nzo 6px3 7crp 7crq 7crr 6
Rad4
(PF03835.17)
2qsg 2qsh 4yir 6cfi 6ubf 5
TFIIB
(PF00382.21)
5fyw 5fz5 6gyl 6gym 6
AAA
(PF00004.31)
6wgc 7jgs 7jk2 7jk5 4
WD40
(PF00400.34)
6r8y 6r90 6r91 6r92 4
RNA_pol_Rpb2_6
(PF00562.30)
5w64 6gmh 6rrd 6tps 4
PCNA_N
(PF00705.20)
3k4x 6eht 6knc 6s1m 4
PWWP
(PF00855.19)
5xsk 6iir 6iis 6iit 4
RAG2
(PF03089.16)
6dbo 6dbw 6oer 6xnx 4
ResIII
(PF04851.17)
5iy6 5iy7 6o9l 6ro4 4
ORC3_N
(PF07034.13)
7jgr 7jk3 7jk4 7jk5 4
PDDEXK_1
(PF12705.9)
3u4q 4ceh 4cei 4cej 4
AAA_22
(PF13401.8)
2qby 7jgr 7jk3 7jk4 4
FtsK_SpoIIIE
(PF01580.20)
6t8b 6t8g 6t8o 7
MCM
(PF00493.25)
5v8f 6f0l 6wgi 4
PCNA_C
(PF02747.17)
3k4x 6knb 6knc 4
Thioredoxin
(PF00085.22)
1t8e 2ajq 6p7e 3
HMG_box
(PF00505.21)
6t7a 6t7c 6t7d 3
TFIIE_alpha
(PF02002.19)
5fz5 6gyl 6gym 3
NusG
(PF02357.21)
5ms0 6c6t 6c6u 3
RNA_pol_A_CTD
(PF03118.17)
6oul 6psv 7khc 3
Cas_Cas5d
(PF09704.12)
5u07 5u0a 6c66 3
IMS_HHH
(PF11798.10)
3gim 3pw4 4f4w 3
ORC5_C
(PF14630.8)
6wgc 6wgg 6wgi 3
Histone_H2A_C
(PF16211.7)
1aoi 6jr0 6la8 3
Bac_DNA_binding
(PF00216.23)
6o6k 6o8q 4
NikR_C
(PF08753.13)
2hzv 6mrj 4
RPOL_N
(PF14700.8)
1h38 1s0v 4
DNA_gyraseB_C
(PF00986.23)
3ksa 6rks 3
zf-H2C2_2
(PF13465.8)
2wbs 5yel 3
MCM_OB
(PF17207.5)
6f0l 6u0m 3
RVT_1
(PF00078.29)
2hmi 3v81 2
DNA_methylase
(PF00145.19)
3pta 6pa7 2
Metallophos
(PF00149.30)
4tug 4tui 2
UvrD-helicase
(PF00580.23)
2is2 6ppr 2
DNA_photolyase
(PF00875.20)
5zcw 6fn0 2
DNA_ligase_ZBD
(PF03119.18)
2owo 4glx 2
RNA_pol_Rpb5_N
(PF03871.16)
3m4o 6eu1 2
RNA_pol_I_TF
(PF04090.14)
5oa1 6tps 2
C2-set_2
(PF08205.14)
4oi7 4oi8 2
VRR_NUC
(PF08774.13)
4ri9 5y7g 2
BTD
(PF09270.12)
1ttu 3brg 2
Cas_CT1975
(PF09344.12)
5h9f 6c66 2
Cas_Csy2
(PF09614.12)
6b44 6ne0 2
Ig_3
(PF13927.8)
4oi7 4oi8 2
HHH_6
(PF14579.8)
4iqj 5fkw 2
DNA_pol_B_palm
(PF14792.8)
2ihm 8icy 2
ERCC3_RAD25_C
(PF16203.7)
5fmf 6gym 2
DUF4918
(PF16265.7)
1oe5 1oe6 2
SH3_11
(PF18103.3)
3l2q 6rny 2
DDE_2
(PF02914.17)
4fcy 4
Vir_act_alpha_C
(PF10400.11)
5x11 4
PHD_4
(PF16866.7)
6asb 3
RCC1
(PF00415.20)
3mvd 2
HTH_Tnp_Mu_1
(PF02316.18)
4fcy 2
HIN
(PF02760.17)
4qgu 2
DNA_gyraseA_C
(PF03989.15)
6rkw 2
Polyoma_lg_T_C
(PF06431.13)
4gdf 2
Cas_Csn2
(PF09711.12)
6qxf 2
AAA_31
(PF13614.8)
5u1j 2
cNMP_binding
(PF00027.31)
3mzh 1
zf-C4
(PF00105.20)
6bqu 1
RecA
(PF00154.23)
7jy9 1
SNF2-rel_dom
(PF00176.25)
6kw4 1
Resolvase
(PF00239.23)
5cy2 1
Helicase_C
(PF00271.33)
6m6b 1
SRF-TF
(PF00319.20)
6wc2 1
RrnaAD
(PF00398.22)
6erq 1
Linker_histone
(PF00538.21)
6la9 1
PHD
(PF00628.31)
6lqf 1
DNA_pol3_beta
(PF00712.21)
5fkv 1
CBFD_NFYB_HMF
(PF00808.25)
4wzs 1
RNase_T
(PF00929.26)
5m1s 1
RNA_pol_A_bac
(PF01000.28)
6n4c 1
RNA_pol_L
(PF01193.26)
6n4c 1
Transposase_1
(PF01359.20)
4u7b 1
N6_N4_Mtase
(PF01555.20)
6pbd 1
Integrase_Zn
(PF02022.21)
6voy 1
MethyltransfD12
(PF02086.17)
1yf3 1
N6_Mtase
(PF02384.18)
7btq 1
SMC_N
(PF02463.21)
6zz6 1
DNA_pol3_beta_2
(PF02767.18)
5m1s 1
BAF
(PF02961.16)
2bzf 1
TAL_effector
(PF03377.15)
4cja 1
PolC_DP2
(PF03833.15)
6knb 1
RNA_pol_Rpc34
(PF05158.14)
6cnc 1
RNA_pol_Rpc82
(PF05645.15)
6cnb 1
TFIIF_alpha
(PF05793.14)
5sva 1
RusA
(PF05866.13)
2h8c 1
Tfb5
(PF06331.14)
5fmf 1
zf-FPG_IleRS
(PF06827.16)
4cis 1
RuvA_C
(PF07499.15)
1c7y 1
PriCT_1
(PF08708.13)
3vw4 1
CRISPR_assoc
(PF08798.13)
5u0a 1
Cdc6_C
(PF09079.13)
7jgr 1
Neil1-DNA_bind
(PF09292.12)
5itu 1
RNA_ligase
(PF09414.12)
2hvr 1
CRISPR_Cse2
(PF09485.12)
6c66 1
SbcD_C
(PF12320.10)
6s85 1
Tet_JBP
(PF12851.9)
5deu 1
AAA_16
(PF13191.8)
2v1u 1
FtsK_alpha
(PF17854.3)
6t8b 1
Cas9_b_hairpin
(PF17893.3)
6joo 1
RecC_C
(PF17946.3)
6sje 1
FANC_SAP
(PF18081.3)
5z6w 1
SRA
(PF18491.3)
4pba 1
RAMA
(PF18755.3)
6pbd 1


SCOP domains
Note: this data is based only on structures available at the moment of the last SCOP release (2009)
Export table
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
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