Interaction mode
Mode:  H-Bb 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
RNA_pol_Rpb1_5
(PF04998.19)
2ja8 2o5i 2o5j 2ppb 2r7z 4a3j 4a3l 4g7h 4g7o 4g7z 4oin 4oiq 4oir 4q4z 4q5s 4wqs 5d4c 5d4d 5d4e 5e17 5e18 5flm 5ipl 5ipm 5ipn 5iy9 5iyd 5m5y 5uh5 5uh8 5uh9 5uha 5uhb 5uhc 5uhd 5uhf 5vo8 5voi 5vvr 5w5y 5w64 5w65 5x21 5x22 5zx2 6asx 6b6h 6cuu 6dv9 6dvb 6dvc 6dvd 6dve 6hko 6hlq 6hlr 6j9e 6j9f 6jbq 6jcx 6jcy 6kon 6koo 6kop 6koq 6kqd 6kqe 6kqf 6kqg 6kqh 6kql 6kqm 6kqn 6l74 6m6c 6omf 6ovr 6ovy 6ow3 6oy5 6oy6 6oy7 6p18 6p19 6p70 6p71 6pb6 6pmi 6pmj 6psw 6tye 6wox 6woy 6wvj 7chw 117
RNA_pol_Rpb1_1
(PF04997.14)
2nvq 2vum 3m4o 3po2 4a3c 4a3d 4a3f 4a3g 4a3k 4a3l 4a3m 4bxx 4by1 4by7 4g7h 4g7z 4oin 4oip 4oiq 4oir 4q4z 4v1m 5d4c 5d4d 5d4e 5e17 5e18 5m5y 5uha 5uhb 5uhe 5uhg 5x21 5x22 6exv 6f42 6kqd 6kqe 6kqf 6kqg 6kqh 6kql 6kqn 6l74 6lts 6ovr 6ow3 6oy6 6oy7 6p71 6pb4 6pmi 6upx 6upy 6upz 6uq2 6uq3 6wox 6woy 6xav 64
DNA_gyraseB_C
(PF00986.23)
2xcr 2xcs 2xct 2xkk 3k9f 3ltn 3rad 3rae 3raf 4bul 4i3h 4juo 4koe 4kpe 4kpf 4plb 4z2c 4z2d 4z2e 4z3o 4z4q 4z53 5bs8 5bta 5btc 5btd 5btf 5btg 5bti 5btl 5btn 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5eix 5iwi 5iwm 6fm4 6fqv 6qtk 6qtp 6qx1 6qx2 6rkv 6z1a 110
HHH_8
(PF14716.8)
1bpz 1xsp 2fmp 2pfq 3jpo 3jpp 3jpq 3jps 3rjf 4klq 4klt 4rq2 4rt3 5bom 5bpc 5ugo 6bel 6bte 6ctl 6ctv 6cub 6mr8 6nku 6nkv 6nkw 6nl0 6pkz 6uom 28
H2TH
(PF06831.16)
1kfv 1l1t 1l1z 1l2b 1l2c 1nnj 1pjj 1pm5 2xzf 2xzu 3a46 3c58 3vk7 3vk8 4nrw 4pcz 4pd2 5itr 5itt 5itu 5itx 6h0s 6rnm 6rnr 6ro2 6rok 35
IMS
(PF00817.22)
1s0o 1s97 1t3n 2r8j 2xgp 2xgq 3gii 3gij 3gil 3gqc 3khr 3pr4 3rb0 3rb3 4irk 4jv2 4qw9 4rzr 5yuw 5yuz 5yv3 6m7p 25
Sigma70_r3
(PF04539.18)
5vi5 6b6h 6edt 6k4y 6kj6 6n60 6n61 6n62 6omf 6oul 6pb4 6pb5 6psq 6vvy 6wmu 6wrd 6wrg 7c17 7ckq 7khb 7khe 7khi 22
RVT_connect
(PF06815.15)
1n6q 1rtd 1t05 3jsm 3jyt 3kjv 3kk1 3kk3 3klf 3klg 3v6d 3v81 6an8 6ika 6kdk 6p1i 6p1x 6p2g 6uir 6uis 6uk0 23
DNA_pol_B_exo1
(PF03104.21)
4flt 4flu 4flv 4flw 4flx 4flz 4fm0 4fm1 4fm2 4m8o 4ptf 6fwk 6g0a 6h1v 6i8a 6qib 18
TOPRIM_C
(PF16898.7)
3l4k 4fm9 4g0v 4gfh 4j3n 5gwi 5gwj 5gwk 5zad 5zen 5zqf 5zrf 19
Histone
(PF00125.26)
4ym6 5b40 5cpj 5cpk 6kix 6kw5 6ltj 6t7d 7cro 12
zf-C2HE
(PF16278.7)
4ndf 4ndg 4ndh 4ndi 6cvp 6cvq 6cvr 6cvs 6cvt 12
TFIIB
(PF00382.21)
1ais 1d3u 1vol 5fyw 5fz5 5iy6 5iya 6f40 8
TAL_effector
(PF03377.15)
3ugm 4cja 4gjr 4osh 4osi 4osj 4osk 30
Integrase_Zn
(PF02022.21)
5m0q 5m0r 6rwl 6rwm 6rwn 6rwo 6voy 20
UvrD-helicase
(PF00580.23)
2is6 3u44 4c2t 6sje 6sjf 6sjg 6t2v 8
RNA_pol_Rpb2_1
(PF04563.17)
5c4j 6alg 6c6s 6c6t 6flp 6rh3 6ri7 7
IMS_HHH
(PF11798.10)
2r8j 2r8k 2wtf 2xgq 4f4w 4f4x 7
zf-C2H2
(PF00096.28)
5wjq 6ml2 6ml4 6ml5 6ml6 6ml7 6
Topo_C_assoc
(PF14370.8)
1k4t 1rrj 1sc7 1seu 1t8i 1tl8 6
SRF-TF
(PF00319.20)
3mu6 3p57 6byy 6bz1 6wc2 11
DNA_pol_B_thumb
(PF14791.8)
1xsl 4k4g 4nm2 4tus 5v1j 7
zf-H2C2_2
(PF13465.8)
1tf6 2gli 2kmk 5v3m 5wjq 6
DNA_photolyase
(PF00875.20)
2wb2 2wq6 3cvw 3cvx 3cvy 5
Mab-21
(PF03281.16)
5xzb 6cta 6edc 6y5d 6y5e 5
RVT_thumb
(PF06817.16)
3kk1 3v6d 5i42 5j2q 6uk0 5
AAA_16
(PF13191.8)
7jgr 7jgs 7jk2 7jk3 7jk4 5
Ku_C
(PF03730.16)
1jey 5y3r 6erg 6erh 6
CarD_CdnL_TRCF
(PF02559.18)
6edt 6eec 6vvy 6vvz 4
RNA_pol_Rpb5_N
(PF03871.16)
5iy7 5iy8 5iyb 5iyc 4
ERCC3_RAD25_C
(PF16203.7)
5ivw 5iy7 5iy8 5oqj 4
DNApol_Exo
(PF18136.3)
4ztu 4ztz 5c52 5c53 4
PCNA_N
(PF00705.20)
6gis 6s1o 6t8h 6
IN_DBD_C
(PF00552.23)
3jca 6puz 6v3k 4
Bac_DNA_binding
(PF00216.23)
4yex 4yey 6oaj 3
Helicase_C
(PF00271.33)
4tmu 4u7d 6o8f 3
XPG_N
(PF00752.19)
5uzv 5v0b 6grb 3
TFIIE_alpha
(PF02002.19)
5iy7 5iyb 5oqj 3
TFIIF_alpha
(PF05793.14)
5iy6 5iya 6o9l 3
AAA_22
(PF13401.8)
5zr1 6wgc 6wgg 3
DUF2312
(PF10073.11)
6cg8 6k2j 7
DNA_pol3_delta2
(PF13177.8)
3glf 3glg 4
Cas_Cas1
(PF01867.18)
5vvl 5xvo 3
Gal4_dimer
(PF03902.15)
1d66 3coq 3
RNase_H
(PF00075.26)
1n6q 1t05 2
SNF2-rel_dom
(PF00176.25)
5x0x 6tda 2
MCM
(PF00493.25)
6f0l 6wgi 2
XPG_I
(PF00867.20)
5zof 5zog 2
MarR
(PF01047.24)
4aik 5hso 2
PCNA_C
(PF02747.17)
6gis 6s1n 2
HIN
(PF02760.17)
3rnu 5z7d 2
DNA_pol3_beta_2
(PF02767.18)
3bep 5fkw 2
RNA_pol_A_CTD
(PF03118.17)
3iyd 7c17 2
Sigma70_r2
(PF04542.16)
6psq 7c97 2
Sigma70_r4
(PF04545.18)
6pb4 6pmj 2
ResIII
(PF04851.17)
5sva 6gym 2
RNA_pol_Rpc82
(PF05645.15)
6cnc 6eu0 2
RNA_pol_I_A49
(PF06870.14)
5w66 6h68 2
HipA_C
(PF07804.14)
4pu3 4yg7 2
TF_Zn_Ribbon
(PF08271.14)
6f42 6f44 2
UvrD_C
(PF13361.8)
1w36 4cej 2
HEAT_2
(PF13646.8)
5oqo 5oqp 2
ORC5_C
(PF14630.8)
6wgc 6wgg 2
FANCI_S4
(PF14678.8)
6vae 6vaf 2
HTH_Tnp_Mu_1
(PF02316.18)
4fcy 2
Phage_CII
(PF05269.13)
1zs4 2
DUF790
(PF05626.13)
6p4f 2
gp45-slide_C
(PF09116.12)
3u5z 2
Endonuc-dimeris
(PF09124.12)
2qnf 2
FancD2
(PF14631.8)
6vaa 2
AAA
(PF00004.31)
3u5z 1
Homeodomain
(PF00046.31)
3d1n 1
DNA_gyraseB
(PF00204.27)
5j5q 1
Forkhead
(PF00250.20)
4wk8 1
RrnaAD
(PF00398.22)
6erp 1
Linker_histone
(PF00538.21)
7c0j 1
DNA_pol3_beta
(PF00712.21)
3bep 1
CBFD_NFYB_HMF
(PF00808.25)
1jfi 1
HTH_3
(PF01381.24)
4i8t 1
DNA_gyraseA_C
(PF03989.15)
6rkw 1
ORC2
(PF04084.16)
7jk5 1
RNA_pol_Rpb2_3
(PF04565.18)
6vvx 1
RNA_pol_Rpc34
(PF05158.14)
6cnd 1
Phage_antitermQ
(PF06530.14)
6jnx 1
Phi-29_GP16_7
(PF06720.13)
2c5r 1
CPL
(PF08144.13)
4wzw 1
PriCT_1
(PF08708.13)
3vw4 1
NikR_C
(PF08753.13)
2hzv 1
T4-Gluco-transf
(PF09198.12)
1m5r 1
Endonuc-FokI_C
(PF09254.13)
1fok 1
CENP-X
(PF09415.12)
4ne1 1
YqaJ
(PF09588.12)
3slp 1
Cas_Csn2
(PF09711.12)
6qxf 1
Cdd1
(PF11731.10)
1t3n 1
DcpS_C
(PF11969.10)
6cvt 1
Rif1_N
(PF12231.10)
5nw5 1
Cohesin_HEAT
(PF12765.9)
6wg3 1
HTH_18
(PF12833.9)
1d5y 1
HTH_27
(PF13463.8)
5k5o 1
HTH_Crp_2
(PF13545.8)
6pb4 1
HHH_5
(PF14520.8)
6sxb 1
HHH_6
(PF14579.8)
5m1s 1
Myb_DNA-bind_7
(PF15963.7)
6eu0 1
Hfq
(PF17209.5)
5uk7 1
DNA_pol3_finger
(PF17657.3)
3e0d 1
Integrase_H2C2
(PF17921.3)
6rny 1
Exog_C
(PF18026.3)
6iid 1
FANC_SAP
(PF18081.3)
5y7g 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)
1l3u 1l3v 1l5u 1njw 1njx 1nk0 1nk5 1nk8 1nkb 1nkc 1nke 2hhu 2hw3 2pyj 2pzs 15
Eukaryotic DNA topoisomerase I, catalytic core
(d.163.1.2)
1a35 1k4s 1k4t 1rr8 1rrj 1sc7 1seu 1t8i 8
Middle domain of MutM-like DNA repair proteins
(a.156.1.2)
1kfv 1nnj 1pji 1pjj 1pm5 1tdz 1xc8 2opf 9
Leucine zipper domain
(h.1.3.1)
1d66 1dh3 1qp9 1zme 3coq 7
Transcription factor IIB (TFIIB), core domain
(a.74.1.2)
1ais 1d3u 1vol 3
Eukaryotic DNA topoisomerase I, dispensable insert domain
(a.2.8.1)
1a36 1r49 2
Heat-shock transcription factor
(a.4.5.22)
1fyl 1fym 2
DNA-binding N-terminal domain of transcription activators
(a.6.1.3)
1exi 1exj 2
Classic zinc finger, C2H2
(g.37.1.1)
1ubd 1un6 4
AraC type transcriptional activator
(a.4.1.8)
1d5y 3
TBP-associated factors, TAFs
(a.22.1.3)
1jfi 1
MarR-like transcriptional regulators
(a.4.5.28)
1fzp 1
Restriction endonuclease EcoRV
(c.52.1.2)
2rve 1
Restriction endonuclease FokI, C-terminal (catalytic) domain
(c.52.1.12)
1fok 1
SRF-like
(d.88.1.1)
1hbx 1
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