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
(PF04998.16)
5iy9 5x21 4oir 6asx 2o5j 2ppb 5w65 4g7o 5iyd 4oiq 5x22 2o5i 5voi 4g7h 4q4z 6b6h 5d4e 5w5y 4wqs 5d4d 5e18 5flm 5e17 30
RNA_pol_Rpb1_1
(PF04997.11)
5d4e 4a3k 5d4d 4oir 2vum 4q4z 5e17 5e18 4a3f 4a3d 4by1 4a3c 4v1m 6exv 4by7 5x21 6f42 5x22 4g7h 4oiq 3po2 23
DNA_gyraseB_C
(PF00986.20)
5bs8 5bta 4plb 6fqv 5iwm 5bs3 5bti 5btl 5btn 5iwi 5btg 5btc 5btd 5btf 4bul 2xcs 2xcr 2xkk 36
IMS
(PF00817.19)
3rbd 3rb4 3rb3 3m9n 3m9o 3rb0 3pr4 4irk 4qw9 4jv2 4qwb 4qw8 3gii 4qwa 3gij 4rzr 1t3n 17
Mab-21
(PF03281.13)
5xzg 4k97 4k99 5xze 4k96 4k98 4k9a 4k9b 4lez 5xzb 11
RVT_connect
(PF06815.12)
3kjv 3kk3 3klf 3klg 3jyt 3jsm 1t05 1rtd 1n6q 3v6d 10
TFIIB
(PF00382.18)
5iy6 5fz5 5fyw 1d3u 5iya 6eu0 6f40 1vol 8
SRF-TF
(PF00319.17)
3mu6 6byy 1egw 6bz1 3p57 1n6j 11
TAL_effector
(PF03377.12)
4osj 4osk 4osi 3ugm 4osh 36
Topo_C_assoc
(PF14370.5)
1k4t 1rrj 1sc7 1seu 1t8i 5
RNA_pol_Rpb5_N
(PF03871.13)
5iyb 5iy7 5iy8 5iyc 4
ERCC3_RAD25_C
(PF16203.4)
5ivw 5oqj 5iy7 5iy8 4
UvrD-helicase
(PF00580.20)
1w36 2is6 3u44 4
TOPRIM_C
(PF16898.4)
4gfh 4fm9 2rgr 4
Histone
(PF00125.23)
3c1c 4ym6 5b40 3
TFIIE_alpha
(PF02002.16)
5iy7 5iyb 5oqj 3
Forkhead
(PF00250.17)
4wk8 2a07 3
Integrase_Zn
(PF02022.18)
5m0q 5m0r 3
RNase_H
(PF00075.23)
1n6q 1t05 2
HSF_DNA-bind
(PF00447.16)
1fym 1fyl 2
MarR
(PF01047.21)
4aik 5hso 2
Sigma70_r3
(PF04539.15)
5vi5 6b6h 2
TFIIF_alpha
(PF05793.11)
5iy6 5iya 2
RVT_thumb
(PF06817.13)
5i42 3kk1 2
DNA_pol3_delta2
(PF13177.5)
3glf 3glg 2
rve
(PF00665.25)
5m0q 2
Cas_Cas1
(PF01867.15)
5xvo 2
HTH_Tnp_Mu_1
(PF02316.15)
4fcy 2
Gal4_dimer
(PF03902.12)
3coq 2
Phage_CII
(PF05269.10)
1zs4 2
gp45-slide_C
(PF09116.9)
3u5z 2
Endonuc-dimeris
(PF09124.9)
2qnf 2
AAA
(PF00004.28)
3u5z 1
Homeobox
(PF00046.28)
3d1n 1
zf-C2H2
(PF00096.25)
5wjq 1
SNF2_N
(PF00176.22)
5x0x 1
RrnaAD
(PF00398.19)
6erp 1
MCM
(PF00493.22)
6f0l 1
IN_DBD_C
(PF00552.20)
3jca 1
XPG_N
(PF00752.16)
5uzv 1
CBFD_NFYB_HMF
(PF00808.22)
1jfi 1
HTH_3
(PF01381.21)
4i8t 1
DNA_pol3_beta_2
(PF02767.15)
5fkw 1
DNA_pol_B_exo1
(PF03104.18)
4ptf 1
Ku_C
(PF03730.13)
1jey 1
RNA_pol_Rpb2_1
(PF04563.14)
6flp 1
ResIII
(PF04851.14)
5sva 1
RNA_pol_Rpc82
(PF05645.12)
6eu0 1
RNA_pol_I_A49
(PF06870.11)
5w66 1
DNA_pol3_alpha
(PF07733.11)
5fkw 1
CPL
(PF08144.10)
4wzw 1
TF_Zn_Ribbon
(PF08271.11)
6f42 1
NikR_C
(PF08753.10)
2hzv 1
Endonuc-FokI_C
(PF09254.10)
1fok 1
MerR-DNA-bind
(PF09278.10)
2zhg 1
YqaJ
(PF09588.9)
3slp 1
Sulf_coat_C
(PF12193.7)
3j9x 1
Rif1_N
(PF12231.7)
5nw5 1
HTH_18
(PF12833.6)
1d5y 1
UvrD_C
(PF13361.5)
4cej 1
HTH_Crp_2
(PF13545.5)
3mzh 1
HHH_6
(PF14579.5)
5m1s 1
DNA_pol_B_thumb
(PF14791.5)
4tus 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)
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
© NPIDB team 2003 - 2019

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