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
IMS
(PF00817.19)
3gii 3gij 4irk 3rbd 3rb0 4jv2 3pr4 3rb4 3rb3 4qwb 1s0n 3m9o 1s0o 1t3n 4qw8 4qw9 4rzr 4qwa 18
RNA_pol_Rpb1_5
(PF04998.16)
2ppb 4q4z 4wqs 2o5j 5d4d 2o5i 5d4e 4g7h 4oiq 4oir 5iy9 4g7z 5iyd 5flm 17
RNA_pol_Rpb1_1
(PF04997.11)
3po2 2vum 4g7h 4g7z 5d4e 4a3f 4q4z 4by7 4by1 4oip 5d4d 4oir 2ppb 4oiq 15
RVT_connect
(PF06815.12)
1t05 1n6q 1rtd 3kk3 3jyt 3klf 3kjv 3klg 3jsm 3v6d 3v81 12
Mab-21
(PF03281.13)
4k96 4k9a 4k97 4k99 4k98 4lez 4k9b 8
TFIIB
(PF00382.18)
5iy6 5fz5 1d3u 1vol 5iya 5fyw 6
TAL_effector
(PF03377.12)
4osh 4osj 4osi 4osk 3ugm 36
RNA_pol_Rpb5_N
(PF03871.13)
5iyc 5iy7 5iy8 5iyb 4
Topo_C_assoc
(PF14370.5)
1t8i 1rrj 1sc7 1k4t 4
SRF-TF
(PF00319.17)
3mu6 3p57 1n6j 8
ERCC3_RAD25_C
(PF16203.4)
5iy8 5iy7 5ivw 3
Forkhead
(PF00250.17)
2a07 4wk8 3
UvrD-helicase
(PF00580.20)
2is6 3u44 3
Gal4_dimer
(PF03902.12)
1d66 3coq 3
Endonuc-dimeris
(PF09124.9)
2qnc 2qnf 3
DNA_pol3_delta2
(PF13177.5)
3glf 3glg 3
Homeobox
(PF00046.28)
5edn 3d1n 2
RNase_H
(PF00075.23)
1n6q 1t05 2
Histone
(PF00125.23)
4ym6 5b40 2
HSF_DNA-bind
(PF00447.16)
1fym 1fyl 2
TFIIE_alpha
(PF02002.16)
5iyb 5iy7 2
Topoisom_I_N
(PF02919.14)
1t8i 1k4t 2
TFIIF_alpha
(PF05793.11)
5iy6 5iya 2
RVT_thumb
(PF06817.13)
3kk1 5i42 2
Phage_CII
(PF05269.10)
1zs4 2
gp45-slide_C
(PF09116.9)
3u5z 2
AAA
(PF00004.28)
3u5z 1
Metallophos
(PF00149.27)
4tui 1
IN_DBD_C
(PF00552.20)
3jca 1
CBFD_NFYB_HMF
(PF00808.22)
1jfi 1
DNA_gyraseB_C
(PF00986.20)
2xkk 1
MarR
(PF01047.21)
4aik 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
RepA_N
(PF06970.10)
5kbj 1
CPL
(PF08144.10)
4wzw 1
NikR_C
(PF08753.10)
2hzv 1
Endonuc-FokI_C
(PF09254.10)
1fok 1
YqaJ
(PF09588.9)
3slp 1
IMS_HHH
(PF11798.7)
2w9b 1
Sulf_coat_C
(PF12193.7)
3j9x 1
HTH_18
(PF12833.6)
1d5y 1
UvrD_C
(PF13361.5)
4cej 1
HTH_Crp_2
(PF13545.5)
3mzh 1
DNA_pol_B_thumb
(PF14791.5)
4tus 1
TOPRIM_C
(PF16898.4)
2rgr 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 - 2017

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