Interaction mode
Mode:  H-Bb L-Bb 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), loop(s) (L) with DNA backbone atoms (Bb).
Pfam domains
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Pfam Domain Family PDB entries Number of structures
IMS_HHH
(PF11798.7)
4rua 4ruc 4rzr 2r8h 2r8g 2j6u 2jef 2jeg 2jei 4tqr 2jej 2oh2 4tqs 2r8i 2rdj 4qwa 4qw9 4qw8 4q44 4q43 2v4r 2v9w 4qwb 4qwc 4r8u 2uvr 2uvu 2uvv 2uvw 4qwe 4qwd 2v4q 2va2 1jx4 1s97 1s9f 2ia6 3pw5 2ago 5edw 1n56 1ryr 1rys 1s0m 1s0n 1s0o 1s10 2agp 2c22 2c28 2c2d 2c2e 2c2r 2asd 2ibk 2imw 2j6s 5c5j 2agq 2asj 2asl 2atl 2bq3 2bqr 2bqu 2br0 2j6t 4irk 4gc6 3khr 4fbt 3m9m 3m9n 3m9o 3pr4 4f4z 4gc7 4ird 4irc 4ir9 4ir1 3khh 3pr5 3pvx 3rb0 3rb3 3rb4 3rbd 3t5l 3t5k 3t5j 3t5h 3rax 3pw0 3pw2 3pzp 3v6h 3qz7 3raq 4juz 2va3 2xcp 3rbe 3gii 3gij 3gil 3gik 2xca 2xc9 2w7o 2w7p 2w8k 2w8l 2w9a 2w9b 2w9c 4jv1 3in5 4jv0 4jv2 155
DNA_pol_lambd_f
(PF10391.8)
4kld 4klg 4klh 4kli 4klj 4jwn 4f5p 4f5o 4f5n 4f5r 4gxk 3tfr 4gxi 3tfs 4jwm 5eoz 4uaw 4tus 4tur 4tuq 4tup 4rq8 4rq6 4rq3 4rq2 4rq0 4rpx 4r66 4r65 4r64 4uay 4ub1 4ub2 4p2h 5bpc 5bom 5bol 4z6f 4z6e 4z6d 4yn4 4ymo 4ymm 4ubc 4ub5 4ub4 4ub3 4r63 4ppx 4mfa 4mf8 4mf2 4m9n 4m9l 4m9h 4m9g 4m47 4m2y 4lvs 4klu 4klt 4klo 4klm 4mfc 4mff 4nlk 4php 4phe 4phd 4pha 4pgx 4pgq 4o9m 4o5k 4o5e 4o5c 4ny8 4nxz 4nlz 4nln 4kll 1tva 3rje 2p66 2fmq 3isb 3gdx 3c2l 3c2m 2fms 1tv9 3rjf 3rji 1bpz 3c2k 4ymn 3lk9 3isd 3isc 1bpx 4gxj 102
RNase_H
(PF00075.23)
5hlf 5hp1 5hro 5d3g 3klf 3klg 3klh 3v81 3v6d 3v4i 3kk1 5i3u 5i42 1j5o 5j2q 25
RVT_thumb
(PF06817.13)
5hro 3klh 3kk2 3kjv 1t03 1rtd 5d3g 5hp1 5i3u 5hlf 2hmi 1r0a 1n5y 1j5o 1n6q 20
Histone
(PF00125.23)
5cpi 3azl 5cpk 3azj 2fj7 3azh 3azf 1p3k 3kwq 3w99 3w98 3o62 3av2 3ayw 3w97 15
TFIIB
(PF00382.18)
5iy7 5iyb 5iyc 1c9b 5iy8 1vol 12
HHH_6
(PF14579.5)
3f2d 3e0d 3f2b 3f2c 5fkv 5
UvrD_C
(PF13361.5)
2is4 4c2u 2is6 4c30 9
UvrD-helicase
(PF00580.20)
3k70 1w36 4c2t 5ld2 6
DNA_pol3_delta2
(PF13177.5)
3gli 3glf 3glg 13
Mab-21
(PF03281.13)
4ley 4lez 4kb6 6
Topo_C_assoc
(PF14370.5)
1rr8 1lpq 1r49 3
AAA
(PF00004.28)
3u60 3u5z 9
zf-C2HE
(PF16278.4)
3spl 3spd 6
Cas_Cas1
(PF01867.15)
5ds4 5dqt 3
RNA_pol_A_CTD
(PF03118.14)
3n97 5ciz 3
Cas_Cas2CT1978
(PF09707.9)
5dlj 5ds6 3
IMS
(PF00817.19)
4qwd 1rys 2
P53
(PF00870.17)
1tup 1tsr 2
UDG
(PF03167.18)
3uob 3uo7 2
H2TH
(PF06831.13)
2f5p 3gq5 2
ParB
(PF08775.9)
3w2a 1zx4 2
HhH-GPD
(PF00730.24)
3cwa 3
DNA_methylase
(PF00145.16)
3pt6 2
DNA_gyraseB_C
(PF00986.20)
3ksb 2
HIN
(PF02760.14)
3rnu 2
ABC_tran
(PF00005.26)
3pih 1
DNA_pol_B
(PF00136.20)
3rmc 1
Metallophos
(PF00149.27)
4tug 1
SNF2_N
(PF00176.22)
1z63 1
HMG_box
(PF00505.18)
4nnu 1
RNase_T
(PF00929.23)
4fzx 1
HTH_3
(PF01381.21)
3zkc 1
Toprim
(PF01751.21)
3ksb 1
MethyltransfD12
(PF02086.14)
1yf3 1
Endonuclease_1
(PF04231.12)
2ivk 1
DNA_ligase_A_N
(PF04675.13)
3l2p 1
ResIII
(PF04851.14)
4zcf 1
RNA_pol_Rpb1_1
(PF04997.11)
2o5i 1
RNA_pol_Rpb1_5
(PF04998.16)
2ppb 1
RusA
(PF05866.10)
2h8c 1
RVT_connect
(PF06815.12)
5hp1 1
DNA_pol3_alpha
(PF07733.11)
5fkv 1
YqaJ
(PF09588.9)
4wuz 1
HHH_2
(PF12826.6)
4bxo 1
Type2_restr_D3
(PF16902.4)
1fok 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
DNA polymerase beta, N-terminal domain-like
(a.60.6.1)
1bpx 1bpy 1bpz 1mq2 1mq3 1rzt 1tv9 1tva 1xsl 1xsn 1xsp 1zjm 1zjn 2fmp 2fmq 2fms 2gws 2iso 2isp 2p66 2pfn 2pfo 2pfp 2pfq 2pxi 3c2k 3c2l 3c2m 3c5g 39
DNA repair glycosylase, 2 C-terminal domains
(a.96.1.3)
1yqr 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu 3d4v 11
Eukaryotic DNA topoisomerase I, catalytic core
(d.163.1.2)
1a31 1lpq 1nh3 1r49 1rr8 1rrj 1seu 1tl8 8
Transcription factor IIB (TFIIB), core domain
(a.74.1.2)
1ais 1c9b 1vol 7
Nucleosome core histones
(a.22.1.1)
1kx4 1zla 2
Endonuclease III
(a.96.1.1)
1orn 1orp 2
p53 DNA-binding domain-like
(b.2.5.2)
1tsr 1tup 2
DnaQ-like 3'-5' exonuclease
(c.55.3.5)
1nk9 4bdp 2
T7 RNA polymerase
(e.8.1.3)
1s76 1s77 2
Myb/SANT domain
(a.4.1.3)
1msf 1
AraC type transcriptional activator
(a.4.1.8)
1d5y 2
CAP C-terminal domain-like
(a.4.5.4)
3e6c 1
Restriction endonuclease FokI, N-terminal (recognition) domain
(a.4.5.12)
1fok 1
TBP-associated factors, TAFs
(a.22.1.3)
1jfi 1
C-terminal domain of RNA polymerase alpha subunit
(a.60.3.1)
1lb2 2
Trp repressor, TrpR
(a.4.12.1)
1trr 4
Restriction endonuclease EcoRV
(c.52.1.2)
2rve 1
C5 cytosine-specific DNA methylase, DCM
(c.66.1.26)
1dct 2
SRF-like
(d.88.1.1)
1hbx 1
Classic zinc finger, C2H2
(g.37.1.1)
1un6 1
Erythroid transcription factor GATA-1
(g.39.1.1)
2gat 1
Leucine zipper domain
(h.1.3.1)
1d66 1
© NPIDB team 2003 - 2017

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