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
Export table
Pfam Domain Family PDB entries Number of structures
DNA_pol_lambd_f
(PF10391.11)
1bpx 1bpy 1bpz 1huo 1huz 1mq2 1mq3 1tv9 1tva 1xsl 1xsn 1zjm 1zjn 1zqa 1zqb 1zqc 1zqd 1zqe 1zqf 1zqg 1zqh 1zqi 1zqj 1zqk 1zql 1zqm 1zqn 1zqo 1zqp 1zqq 1zqr 1zqs 1zqt 2bpf 2bpg 2fmp 2fmq 2fms 2gws 2i9g 2ihm 2iso 2isp 2p66 2pfq 2pxi 3c2k 3c2l 3c2m 3c5f 3c5g 3gdx 3hx0 3isb 3isc 3isd 3jpn 3jpo 3jpp 3jpq 3jpr 3jps 3jpt 3lk9 3mby 3mda 3mgh 3mgi 3ogu 3pml 3pmn 3pnc 3rh4 3rh5 3rh6 3rje 3rjf 3rjg 3rjh 3rji 3rjj 3rjk 3tfr 3tfs 3uq0 3uxp 3v72 3v7j 3v7k 4do9 4doa 4dob 4doc 4f5n 4f5o 4f5p 4f5q 4f5r 4gxi 4gxj 4gxk 4jwm 4jwn 4k4g 4k4h 4k4i 4kld 4kle 4klf 4klg 4klh 4kli 4klj 4kll 4klm 4klo 4klq 4kls 4klt 4klu 4lvs 4m2y 4m47 4m9g 4m9h 4m9j 4m9l 4m9n 4mf2 4mf8 4mfa 4mfc 4mff 4nlk 4nln 4nlz 4nm1 4nm2 4nxz 4ny8 4o5c 4o5e 4o5k 4o9m 4p2h 4pgq 4pgx 4pgy 4ph5 4pha 4phd 4phe 4php 4ppx 4r63 4r64 4r65 4r66 4rpx 4rpy 4rpz 4rq0 4rq1 4rq2 4rq3 4rq4 4rq5 4rq6 4rq7 4rq8 4rt2 4rt3 4tup 4tuq 4tur 4tus 4uaw 4uay 4uaz 4ub1 4ub2 4ub3 4ub4 4ub5 4ubb 4ubc 4xq8 4xrh 4ymm 4ymn 4ymo 4yn4 4z6c 4z6d 4z6e 4z6f 5bol 5bom 5bpc 5ca7 5chg 5cj7 5cp2 5cr0 5cwr 5db6 5db7 5db8 5db9 5dba 5dbb 5dbc 5ddm 5dkw 5eoz 5hhh 5hhi 5iii 5iik 5iio 5j0o 5j0p 5j0q 5j0r 5j0s 5j0t 5j0u 5j0w 5j0x 5j0y 5j29 5j2a 5j2b 5j2c 5j2d 5j2e 5j2f 5j2g 5j2h 5j2i 5j2j 5j2k 5tb8 5tb9 5tba 5tbb 5tbc 5tzv 5u2r 5u2s 5u2t 5u8g 5u8h 5u8i 5u9h 5ugn 5ugo 5ugp 5v1f 5v1g 5v1h 5v1i 5v1j 5v1n 5v1o 5v1p 5v1r 5vez 5vrw 5vrx 5vry 5vrz 5vs0 5vs1 5vs2 5vs3 5vs4 5wnx 5wny 5wnz 5wo0 6bel 6bem 6bte 6btf 6cly 6cpq 6cr3 6cr4 6cr5 6cr6 6cr7 6cr8 6cr9 6crb 6crc 6crh 6cti 6ctj 6ctk 6ctl 6ctm 6ctn 6cto 6ctp 6ctq 6ctr 6ctt 6ctu 6ctv 6ctw 6ctx 6cu9 6cua 6cub 6dia 6dic 6e3r 6e3v 6e3w 6e3x 6g2q 6go5 6mr7 6mr8 6n2r 6n2s 6n2t 6nkr 6nks 6nkt 6nku 6nkv 6nkw 6nkx 6nky 6nkz 6nl0 6ph5 6ph6 6pkz 6u2o 6u6b 6uok 6uol 6uom 6w2m 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8ica 8icb 8icc 8ice 8icf 8icg 8ich 8ici 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 8icz 9ica 9icb 9icc 9ice 9icf 9icg 9ich 9ici 9icj 9ick 9icl 9icm 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv 9icw 9icx 9icy 443
IMS_HHH
(PF11798.10)
1jx4 1jxl 1n56 1ryr 1rys 1s0m 1s0n 1s0o 1s10 1s97 1s9f 2ago 2agp 2agq 2asd 2asj 2asl 2atl 2bq3 2bqr 2bqu 2br0 2c22 2c28 2c2d 2c2e 2c2r 2ia6 2ibk 2imw 2j6s 2j6t 2j6u 2jef 2jeg 2jei 2jej 2oh2 2r8g 2r8h 2r8i 2r8j 2rdj 2uvr 2uvu 2uvv 2uvw 2v4q 2v4r 2w7o 2w7p 2w8k 2w8l 2w9a 2w9c 2xc9 2xca 2xcp 2xgp 2xgq 3bq0 3bq1 3bq2 3gii 3gij 3gik 3gil 3in5 3khg 3khh 3khl 3khr 3m9m 3m9n 3m9o 3mfh 3mfi 3oha 3ohb 3pr4 3pr5 3pvx 3pw0 3pw2 3pw5 3pw7 3pzp 3qz7 3qz8 3raq 3rax 3rb0 3rb3 3rb4 3rb6 3rbd 3rbe 3t5h 3t5j 3t5k 3t5l 3v6h 3v6j 3v6k 4f4z 4f50 4fbt 4g3i 4gc6 4gc7 4hyk 4ir1 4ir9 4irc 4ird 4irk 4juz 4jv0 4jv1 4jv2 4q43 4q44 4q45 4qw8 4qw9 4qwa 4qwb 4qwc 4qwd 4qwe 4r8u 4rua 4ruc 4rzr 4tqr 4tqs 4u6p 4u7c 5c5j 5edw 5t14 5w2a 5w2c 5yur 5yus 5yut 5yuu 5yuv 5yuw 5yux 5yuy 5yuz 5yv0 5yv1 5yv2 5yv3 5yyd 5yye 5zlv 6brx 6bs1 6cst 6ig1 6jup 6juq 247
RVT_thumb
(PF06817.16)
1j5o 1n5y 1n6q 1r0a 1rtd 1t03 1t05 2hmi 3jsm 3jyt 3kjv 3kk2 3kle 3klf 3klg 3klh 3v4i 3v6d 3v81 4r5p 5d3g 5hlf 5hp1 5hro 5i3u 5j2m 5j2n 5j2p 5txl 5txm 5txn 5txo 5txp 5xn0 5xn2 6amo 6an2 6an8 6anq 6asw 6avm 6avt 6ik9 6ika 6kdj 6kdm 6kdn 6o9e 6or7 6otz 6oun 6p1i 6p1x 6p2g 6uir 6uis 6uit 6ujx 6ujy 6ujz 6wpf 6wph 6wpj 93
Histone
(PF00125.26)
1zla 2fj7 3av2 3ayw 3azf 3azh 3azj 3azl 3kwq 3o62 3w97 3w98 3w99 5cpi 5gse 5gsu 5x0x 5z3l 5z3o 5z3u 5z3v 6jyl 6k1p 6kiv 6kiw 6kix 6kiz 6kw3 6m4d 6nog 6nqa 6o96 6r8y 6r90 6t79 6t7b 6t7d 6ugm 6uxw 6ven 6xjd 6y5d 6y5e 7crp 7crq 7crr 68
RNA_pol_Rpb1_1
(PF04997.14)
2o5i 2ppb 3m3y 4g7o 4q5s 5d4c 5d4e 5uhd 5uhf 5vi5 6b6h 6c6u 6dvb 6dvd 6edt 6ee8 6eec 6eu0 6flp 6gml 6h67 6jcx 6jcy 6koo 6kqd 6kqm 6o6c 6omf 6oul 6ovy 6oy5 6p70 6pb6 6psv 6psw 6ri7 6rip 6vvx 6vvz 6wmu 6wr6 6wr8 6wvj 7khb 7khc 46
H2TH
(PF06831.16)
1k3w 1k3x 1k82 1pji 1r2z 1tdz 1xc8 2ea0 2f5o 2f5p 2f5s 2opf 2oq4 3gpy 3gq3 3gq4 3gq5 3jr5 3sas 3sau 3twm 3u6d 3u6l 3u6o 3u6q 3u6s 4g4n 4g4o 4g4q 4g4r 4pdg 4pdi 5itr 5itu 5ity 6fbu 6rno 6rp0 6rp7 6tc9 47
Cdd1
(PF11731.10)
1t3n 2alz 2dpi 2dpj 2fll 2fln 2flp 3epg 3epi 3g6v 3g6x 3g6y 3gv5 3gv7 3gv8 3h40 3h4b 3h4d 3ngd 3osn 3q8p 3q8q 3q8r 3q8s 4ebc 4ebd 4ebe 4eyh 4eyi 4fs1 4fs2 5kt2 5kt3 5kt4 5kt5 5kt6 5kt7 5ulw 5ulx 40
RNase_H
(PF00075.26)
1j5o 3kk1 3klf 3klg 3klh 3v4i 3v6d 3v81 5d3g 5hlf 5hp1 5hro 5i3u 5i42 5j2q 5txl 5txm 5txn 5txo 5txp 5xn0 6amo 6an2 6anq 6asw 6avm 6avt 6o9e 6or7 6oun 6uis 6ujz 6wpf 6wph 6wpj 51
TFIIB
(PF00382.21)
1ais 1c9b 1vol 5iy7 5iy8 5iyb 5iyc 6cnb 6cnd 6cnf 6eu0 6f40 6f41 6f42 6f44 6o9l 24
RNA_pol_A_CTD
(PF03118.17)
3n4m 3n97 5ciz 5tw1 6b6h 6ccv 6psq 6psr 6pss 6pst 6psw 6vvv 6wr6 7khc 17
IMS
(PF00817.22)
1rys 2r8j 2w7o 2w7p 2xgq 3h40 4juz 4tqs 5l1i 5w2a 5w2c 6juo 6juq 6jus 15
SNF2-rel_dom
(PF00176.25)
1z63 5vvr 5x0y 5z3o 5z3u 5z3v 6iro 6k1p 6ne3 6uxw 6vz4 12
HHH
(PF00633.25)
1rrq 1rrs 1vrl 3g0q 4yoq 4yph 4ypr 5kn8 5kn9 6q0c 6u7t 12
HHH_8
(PF14716.8)
3rh6 3tfr 3tfs 4r65 4rt2 5j29 6cr3 6cr4 6ctk 6ctq 6ctw 11
Mab-21
(PF03281.16)
4k96 4k97 4k9a 4k9b 4kb6 4ley 5n6i 5xze 6ct9 6edb 15
RNA_pol_Rpb1_5
(PF04998.19)
2o5j 2ppb 6ldi 6pb4 6rh3 6ri9 6vw0 6xav 7c17 7khb 11
DcpS_C
(PF11969.10)
4ndf 4ndg 4ndh 4ndi 6cvp 6cvq 6cvr 6cvs 6cvt 17
Toprim
(PF01751.24)
3ksa 3ksb 4gfh 4i3h 4z2c 4z2d 4z2e 5cdq 6fqv 10
CENP-T_C
(PF15511.8)
5z3l 6iy2 6kiv 6ne3 6nqa 6t7a 6t7c 6xjd 6y5d 10
AAA
(PF00004.31)
3u5z 3u60 3u61 5zr1 7jgr 7jk3 7jk4 7jps 20
zf-C2HE
(PF16278.7)
3spd 3spl 4ndf 4ndh 4ndi 6cvq 6cvr 6cvs 14
Helicase_C
(PF00271.33)
5x0x 5x0y 5z3l 5z3o 5z3v 6iy2 6iy3 6uxw 8
RNA_pol_I_TF
(PF04090.14)
5w64 5w65 5w66 6rrd 6rui 6ruo 6rwe 7
Myb_DNA-bind_7
(PF15963.7)
6cnb 6cnc 6cnd 6cnf 6f41 6f42 6f44 7
TAL_effector
(PF03377.15)
4cja 4gjr 4osh 4osi 4osj 4osk 36
UvrD_C
(PF13361.8)
2is4 2is6 3k70 4c2t 4c2u 4c30 12
UvrD-helicase
(PF00580.23)
1w36 3k70 4c2t 5ld2 6t2u 7
Topo_C_assoc
(PF14370.8)
1a31 1k4s 1lpq 1r49 1rr8 5
HHH_6
(PF14579.8)
3e0d 3f2b 3f2c 3f2d 5fkv 5
HhH-GPD
(PF00730.27)
3cwa 3ogd 3oh6 3oh9 6
DNA_gyraseB_C
(PF00986.23)
3k9f 3ksb 5iwi 6qtk 5
ORC2
(PF04084.16)
5v8f 6wgc 6wgg 6wgi 4
DNA_ligase_A_N
(PF04675.16)
3l2p 6bkf 6bkg 6p0a 4
RVT_connect
(PF06815.15)
5d3g 5hp1 6ik9 6kdj 4
DNA_pol3_delta2
(PF13177.8)
3glf 3glg 3gli 20
zf-H2C2_2
(PF13465.8)
3uk3 4is1 5v3j 6
Bac_DNA_binding
(PF00216.23)
6o6k 6o8q 6oaj 4
Cas_Cas1
(PF01867.18)
5dqt 5ds4 6opm 4
TOPRIM_C
(PF16898.7)
3qx3 4g0u 5gwk 4
RrnaAD
(PF00398.22)
6erp 6ymv 6ymw 3
DNA_photolyase
(PF00875.20)
2wq7 3cvu 3cvv 3
HTH_3
(PF01381.24)
4pu4 4yg4 6lb3 3
HHH_2
(PF12826.9)
2owo 4bxo 4glx 3
HIN
(PF02760.17)
3rnu 5z7d 4
ResIII
(PF04851.17)
4zcf 6o8g 4
MethyltransfD12
(PF02086.17)
1q0t 1yf3 3
STAT_bind
(PF02864.17)
4y5w 5d39 3
Endonuclease_1
(PF04231.15)
1oup 2ivk 3
Cas_Cas2CT1978
(PF09707.12)
5dlj 5ds6 3
AAA_23
(PF13476.8)
4w9m 6s85 3
HHH_5
(PF14520.8)
1c7y 3auo 3
zf-C2H2
(PF00096.28)
6ki6 6u9q 2
Metallophos
(PF00149.30)
4tug 4tui 2
XPG_I
(PF00867.20)
5v0b 5zoe 2
P53
(PF00870.20)
1tsr 1tup 2
Topoisom_I
(PF01028.22)
1k4s 1nh3 2
SMC_N
(PF02463.21)
6wg3 6yuf 2
UDG
(PF03167.21)
3uo7 3uob 2
RNA_pol_Rpb5_N
(PF03871.16)
6gmh 6ted 2
Sigma70_r4
(PF04545.18)
6pb6 6pmi 2
ParB
(PF08775.12)
1zx4 3w2a 2
T4-Gluco-transf
(PF09198.12)
1m5r 1sxp 2
BHD_1
(PF10403.11)
4yir 6uin 2
Cohesin_HEAT
(PF12765.9)
6wge 6zz6 2
DNA_pol_B_thumb
(PF14791.8)
1huo 3au6 2
FANC_SAP
(PF18081.3)
5y7g 5y7q 2
HMG_box
(PF00505.21)
3nm9 3
zf-C2H2_4
(PF13894.8)
5k5l 3
DNA_methylase
(PF00145.19)
3pt6 2
Forkhead
(PF00250.20)
2a07 2
MarR
(PF01047.24)
5hso 2
DNA_ligase_A_M
(PF01068.23)
2q2u 2
Integrase_Zn
(PF02022.21)
6z2y 2
NDC10_II
(PF16787.7)
6gys 2
zf-C4
(PF00105.20)
6bsf 1
DNA_pol_B
(PF00136.23)
3rmc 1
Resolvase
(PF00239.23)
1gdt 1
Myb_DNA-binding
(PF00249.33)
3ted 1
DEAD
(PF00270.31)
6m6b 1
SRF-TF
(PF00319.20)
6wc2 1
CBFD_NFYB_HMF
(PF00808.25)
1jfi 1
5_3_exonuc
(PF01367.22)
5hnk 1
Y1_Tnp
(PF01797.18)
2vic 1
CarD_CdnL_TRCF
(PF02559.18)
6ee8 1
BamHI
(PF02923.17)
1esg 1
Pyr_excise
(PF03013.16)
1vas 1
DNA_pol_B_exo1
(PF03104.21)
4fly 1
PolC_DP2
(PF03833.15)
6t8h 1
Gal4_dimer
(PF03902.15)
1d66 1
RNA_pol_Rpb2_1
(PF04563.17)
6pst 1
RNA_pol_Rpc34
(PF05158.14)
6cnf 1
RusA
(PF05866.13)
2h8c 1
Phi-29_GP16_7
(PF06720.13)
2c5r 1
ORC3_N
(PF07034.13)
7jps 1
DNA_pol3_alpha
(PF07733.14)
5fkv 1
AsiA
(PF09010.12)
6k4y 1
Cro
(PF09048.12)
3orc 1
Endonuc-dimeris
(PF09124.12)
2qnc 1
YqaJ
(PF09588.12)
4wuz 1
Cas_Csn2
(PF09711.12)
6qxf 1
Cnd3
(PF12719.9)
5oqp 1
AAA_16
(PF13191.8)
7jk5 1
AAA_22
(PF13401.8)
5v8f 1
HTH_Crp_2
(PF13545.8)
3iyd 1
HTH_37
(PF13744.8)
6lty 1
ORC4_C
(PF14629.8)
6wgi 1
Type2_restr_D3
(PF16902.7)
1fok 1
Exog_C
(PF18026.3)
6iid 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
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
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