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
DNA_pol_lambd_f
(PF10391.8)
4rpz 4php 4phe 4phd 4rpy 4pgx 4rq0 4rq3 4pgq 4ppx 4rq2 4rpx 4kls 4r66 4r65 4rq1 4r63 4klq 4r64 4pha 4m47 4m9h 4nln 4nlk 4mfc 4m9j 4m9l 4m9n 4mf2 4mf8 4mfa 4nlz 4m9g 4p2h 4o9m 4o5k 4klt 4o5c 4ny8 4nxz 4klu 4lvs 4m2y 4mff 1bpx 5tbc 5tbb 5tba 5tb8 5ugp 4o5e 1tv9 1tva 5hhi 5hhh 5eoz 5u2r 5u2s 5u2t 1bpz 5wo0 5wnz 5wny 5wnx 5ugo 5ugn 5u9h 5u8i 5u8h 5u8g 5bpc 5bom 5bol 4uaz 4uay 4uaw 4tus 4tur 4tuq 4tup 4rq8 4rq7 4rq6 4rq5 4ub1 4ub2 4ub3 4z6f 4z6e 4z6d 4yn4 4ymo 4ymn 4ymm 4ubc 4ubb 4ub5 4ub4 4rq4 5tb9 4f5r 2fmq 3c2m 3c2l 3c2k 3rji 4gxi 4gxj 3rjf 4f5p 4f5o 2fms 3tfs 3tfr 3isd 3isc 3isb 3lk9 2p66 3gdx 4f5n 4gxk 3rje 4jwm 4jwn 4kld 4klj 4klf 4kli 4klh 4klg 4kle 4kll 4klm 4klo 136
IMS_HHH
(PF11798.7)
2r8h 2uvv 3m9m 2agp 1s9f 2uvu 2uvr 2rdj 2r8i 2r8g 3m9n 3m9o 3raq 3pr5 3qz7 3pw5 3pw2 3pw0 3pvx 2asd 3rax 2oh2 2ago 3pr4 2agq 2jej 5edw 2v9w 1n56 2c22 2v4r 3gii 3gij 2va2 2w7o 2w9c 2xc9 2xca 2xcp 1jx4 2w9a 2w8l 3gik 3gil 1s0m 1s0n 1s0o 3khr 1s10 1s97 3khh 1ryr 1rys 3in5 2v4q 2uvw 2asl 2imw 4qwd 2c28 4qwc 4qwb 4qwa 4qw9 4qw8 4qwe 4f4z 2ibk 3v6h 2ia6 4r8u 4ir1 4q44 4q43 4ir9 4irc 4ird 4irk 4juz 4jv0 4jv1 4fbt 4gc6 4gc7 2c2r 3pzp 2c2e 2c2d 4jv2 3rb0 2jeg 2bqu 3t5h 3t5j 2bqr 3t5k 3t5l 2jef 2jei 3rbe 2atl 5c5j 2bq3 3rb3 3rb4 3rbd 2j6u 2j6s 2br0 4tqs 4tqr 4rua 2j6t 4rzr 4ruc 145
RNase_H
(PF00075.23)
5i3u 5i42 3v6d 5hro 3v4i 5d3g 5hlf 5hp1 5j2q 5txm 5xn0 5txo 5txn 3klg 3klh 5txl 5txp 1j5o 3klf 3kk1 29
Histone
(PF00125.23)
5gse 3azj 5cpk 5cpi 3azh 5gxq 3azf 3ayw 3w97 3w98 3w99 2fj7 5gsu 3o62 5x0x 3av2 1p3k 3kwq 3azl 20
RVT_thumb
(PF06817.13)
5d3g 2hmi 5hp1 5hlf 5hro 3klh 1rtd 5xn0 1n5y 3kk2 5xn2 3kjv 5i3u 1r0a 1t03 1n6q 1j5o 22
TFIIB
(PF00382.18)
1ais 1c9b 5iyc 5iy7 5iy8 1vol 5iyb 6f40 6f42 6f44 12
RNA_pol_A_CTD
(PF03118.14)
3n4m 5tw1 3n97 5vi8 6b6h 7
RNA_pol_Rpb1_1
(PF04997.11)
6flp 4g7o 6b6h 6eu0 5vi5 6
HHH_6
(PF14579.5)
3f2d 5fkv 3f2b 3f2c 3e0d 5
Mab-21
(PF03281.13)
4kb6 4ley 5n6i 4lez 12
Toprim
(PF01751.21)
6fqv 4gfh 5bs3 3ksb 9
UvrD_C
(PF13361.5)
4c30 4c2u 2is4 2is6 7
UvrD-helicase
(PF00580.20)
4c2t 3k70 5ld2 1w36 5
DNA_pol3_delta2
(PF13177.5)
3gli 3glf 3glg 10
SNF2_N
(PF00176.22)
5vvr 5x0y 1z63 4
IMS
(PF00817.19)
1rys 1s0n 4qwd 3
RNA_pol_I_TF
(PF04090.11)
5w64 5w66 5w65 3
Topo_C_assoc
(PF14370.5)
1lpq 1rr8 1r49 3
AAA
(PF00004.28)
3u5z 3u60 9
zf-C2HE
(PF16278.4)
3spd 3spl 6
HMG_box
(PF00505.18)
4nnu 3nm9 3
Cas_Cas1
(PF01867.15)
5dqt 5ds4 3
Cas_Cas2CT1978
(PF09707.9)
5dlj 5ds6 3
P53
(PF00870.17)
1tsr 1tup 2
UDG
(PF03167.18)
3uo7 3uob 2
DNA_ligase_A_N
(PF04675.13)
3l2p 1x9n 2
RNA_pol_Rpb1_5
(PF04998.16)
2ppb 2o5j 2
H2TH
(PF06831.13)
2f5p 3gq5 2
ParB
(PF08775.9)
1zx4 3w2a 2
DNA_methylase
(PF00145.16)
3pt6 2
HhH-GPD
(PF00730.24)
3cwa 2
DNA_gyraseB_C
(PF00986.20)
3ksb 2
MarR
(PF01047.21)
5hso 2
HIN
(PF02760.14)
3rnu 2
AAA_23
(PF13476.5)
4w9m 2
Myb_DNA-bind_7
(PF15963.4)
5n9g 2
ABC_tran
(PF00005.26)
3pih 1
DNA_pol_B
(PF00136.20)
3rmc 1
Metallophos
(PF00149.27)
4tug 1
Helicase_C
(PF00271.30)
5x0y 1
RrnaAD
(PF00398.19)
6erp 1
RNase_T
(PF00929.23)
4fzx 1
DNA_ligase_A_M
(PF01068.20)
1x9n 1
HTH_3
(PF01381.21)
3zkc 1
MethyltransfD12
(PF02086.14)
1yf3 1
DNA_pol_B_exo1
(PF03104.18)
5gnq 1
Endonuclease_1
(PF04231.12)
2ivk 1
ResIII
(PF04851.14)
4zcf 1
RusA
(PF05866.10)
2h8c 1
RVT_connect
(PF06815.12)
5hp1 1
DNA_pol3_alpha
(PF07733.11)
5fkv 1
Endonuc-dimeris
(PF09124.9)
2qnc 1
YqaJ
(PF09588.9)
4wuz 1
Cnd3
(PF12719.6)
5oqp 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 - 2019

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