Interaction mode
Mode:  S-Bb L-Bb 
Description: Conserved protein-DNA contacts are provided by β-strand(s) (S) 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
CENP-T_C
(PF15511.8)
1aoi 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3p 1u35 1zbb 2f8n 2fj7 3ayw 3aze 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3c1c 3kwq 3mvd 3o62 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1v 4qlc 4x23 4xzq 4ym5 4ym6 4ys3 4z5t 4z66 5ay8 5b0y 5b1m 5b24 5b32 5b33 5cpi 5cpk 5e5a 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5jrg 5wcu 5x0x 5x0y 5xm0 5xm1 5y0c 5z23 5z30 5z3l 5z3o 5z3u 5z3v 5zbx 6dzt 6e0c 6e0p 6hkt 6iy2 6j99 6jyl 6k1p 6kiw 6kiz 6kw3 6kw4 6kxv 6la8 6la9 6m3v 6m4d 6m4g 6m4h 6ne3 6nog 6nzo 6o1d 6o96 6om3 6pa7 6pwv 6pww 6pwx 6px1 6px3 6r8y 6r8z 6r90 6r91 6r92 6r93 6r94 6t79 6t7b 6t7d 6t90 6t93 6tda 6ugm 6uh5 6uxw 6v2k 6v92 6x59 6x5a 6y5d 6y5e 6yov 7c0m 7crp 7crr 7k5x 7k5y 7k60 7k61 7k63 245
DNA_pol_B_palm
(PF14792.8)
1bpx 1bpz 1mq2 1mq3 1xsn 1zjn 2bpf 2bpg 2ihm 3c2l 3c5f 3hw8 3mgh 3mgi 3pml 3uq0 3uxp 3v7j 3v7k 4k4g 4k4h 4klq 4kls 4m2y 4mf2 4mf8 4mfa 4mfc 4mff 4nln 4nm2 4ny8 4o5e 4p2h 4p4o 4pgq 4pgy 4phe 4php 4rq1 4tur 4tus 4xq8 4xrh 4ymm 4ymn 4yn4 5ca7 5chg 5cj7 5cp2 5cr0 5cwr 5db7 5db8 5db9 5dba 5dbb 5dbc 5ddm 5eoz 5hhi 5j2a 5tb9 5u2s 5vrw 5vrx 5vry 5vrz 5vs0 5vs1 5vs2 5vs3 6cub 6e3r 6e3x 6go5 6n2s 6nkr 6nks 6nkt 6ph6 6pkz 6uol 7ice 7icg 7ich 7ici 7icj 7icl 7icn 7ico 7icp 7icq 7icr 7ict 7icu 7icv 8ica 8ici 8ico 8icp 8icv 8icw 9ice 9ich 9ick 9icl 9icn 9ico 9icq 9icr 9ics 9ict 9icw 9icx 121
RVT_connect
(PF06815.15)
1j5o 1n5y 1n6q 1r0a 1t03 3kjv 3kk1 3kk2 3kle 3klf 3klg 3klh 3v4i 3v6d 3v81 4r5p 5d3g 5hlf 5hp1 5hro 5i3u 5i42 5j2m 5j2n 5j2p 5j2q 5txl 5txm 5txn 5txo 5txp 5xn0 5xn1 5xn2 6amo 6an2 6an8 6anq 6asw 6avm 6avt 6ik9 6ika 6kdj 6kdk 6kdm 6kdn 6kdo 6o9e 6or7 6otz 6oun 6p1i 6p2g 6uir 6uis 6uit 6ujx 6ujy 6ujz 6wpf 6wph 6wpj 87
IMS_C
(PF11799.10)
1s0m 1s97 1s9f 2alz 2atl 2bqr 2fll 2fln 2j6s 2jef 2uvr 2w7o 2w7p 2w8l 2xcp 3in5 3khh 3pvx 3pw2 3pw4 3pzp 3rb0 4ebc 4fs1 4juz 4qwc 4rzr 4u6p 5edw 5kt6 5t14 5w2c 6brx 6bs1 6jul 6jum 6juo 6jur 40
MutS_III
(PF05192.20)
1e3m 1ewq 1fw6 1ng9 1nne 1oh5 1oh6 1oh7 1oh8 1w7a 1wb9 1wbb 1wbd 2o8b 2o8c 2o8d 2o8e 2o8f 2wtu 3k0s 3thw 3thx 3thy 3zlj 38
IMS
(PF00817.22)
2asl 2imw 2r8k 2uvw 2wtf 2xcp 3khr 3qz8 3t5k 3v6h 3v6j 4q44 4q45 4r8u 5edw 5jum 6cst 6jun 6jup 6jus 6ui2 6uqi 6v5k 25
MutS_IV
(PF05190.20)
1e3m 1ewq 1fw6 1ng9 1nne 1oh5 1oh6 1oh7 1oh8 1w7a 1wb9 1wbb 1wbd 2o8b 2o8c 2o8d 2o8e 2o8f 2wtu 3k0s 3zlj 35
Histone
(PF00125.26)
1id3 3aze 4ym6 5wcu 6kiv 6kix 6kiz 6m44 6om3 6r92 6t7b 6t7c 6y39 7crr 16
TFIIA
(PF03153.15)
1nh2 1nvp 1rm1 5fmf 5fur 5fyw 5fz5 5iy6 5iy8 5iya 5iyc 6mzm 12
IN_DBD_C
(PF00552.23)
5ejk 5u1c 6put 6puw 6puz 6rwl 6rwm 6rwo 6u8q 6vdk 16
zf-FPG_IleRS
(PF06827.16)
1k3x 1l1t 1l1z 1l2b 1l2c 1r2y 1r2z 3gpy 8
DNA_pol_B
(PF00136.23)
2dtu 2dy4 2p5o 3k5n 3rma 3rmd 3taf 7
DNA_pol_B_thumb
(PF14791.8)
5j2i 5vs1 6crb 6ctp 6ph6 6uom 6w2m 7
HIN
(PF02760.17)
3rn2 3rn5 4jbk 4l5r 4l5s 4lnq 9
RHD_dimer
(PF16179.7)
1a3q 1le5 1owr 1p7h 2ram 5u01 7
RAG2
(PF03089.16)
3jby 6dbo 6dbr 6xnx 5
CRISPR_Cas9_WED
(PF18061.3)
5axw 6m0v 6m0w 6rjd 4
Ku
(PF02735.18)
6erf 6erg 6erh 8
PWWP
(PF00855.19)
5xsk 6iiq 6iir 3
zf-H2C2_2
(PF13465.8)
5v3j 6b0o 6dfb 3
Transposase_1
(PF01359.20)
4u7b 5hoo 4
SRA
(PF18491.3)
4par 4pba 3
Cdc6_C
(PF09079.13)
7jgs 7jk2 2
BTD
(PF09270.12)
3nbn 4j2x 2
Neil1-DNA_bind
(PF09292.12)
5itr 5itx 2
Ig_3
(PF13927.8)
4oi7 4oi8 2
Chromo_2
(PF18704.3)
5t9j 3
VRR_NUC
(PF08774.13)
4r89 2
Mu-transpos_C
(PF09299.13)
4fcy 2
Tudor-knot
(PF11717.10)
3oa6 2
RVT_1
(PF00078.29)
3kle 1
Metallophos
(PF00149.30)
6s85 1
Bac_DNA_binding
(PF00216.23)
6o8q 1
TBP
(PF00352.23)
6gyl 1
MCM
(PF00493.25)
5v8f 1
XPG_I
(PF00867.20)
6grb 1
DNA_ligase_A_M
(PF01068.23)
6bkf 1
MBD
(PF01429.21)
3vyq 1
Toprim
(PF01751.24)
6rku 1
Cas_Cas1
(PF01867.18)
5dqu 1
Hjc
(PF01870.20)
2wiw 1
STAT_bind
(PF02864.17)
4y5w 1
DNA_ligase_OB
(PF03120.18)
2owo 1
DNA_gyraseA_C
(PF03989.15)
6rkw 1
RNA_pol_Rpb2_2
(PF04561.16)
6pb5 1
RNA_pol_Rpb2_1
(PF04563.17)
6pb5 1
RNA_pol_Rpb1_5
(PF04998.19)
6jnx 1
RQC
(PF09382.12)
4u7d 1
RNA_ligase
(PF09414.12)
2hvs 1
DUF4918
(PF16265.7)
1oe4 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 repair protein MutS, domain III
(a.113.1.1)
1e3m 1ewq 1fw6 1ng9 1nne 1oh5 1oh6 1oh7 1oh8 1w7a 1wb9 1wbb 1wbd 22
Nucleosome core histones
(a.22.1.1)
1kx3 1kx4 1kx5 2nzd 2pyo 3b6f 3b6g 3c1c 9
N-terminal domain of MutM-like DNA repair proteins
(b.113.1.1)
1l1t 1l1z 1l2c 1l2d 4
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
(b.1.18.1)
1owr 1p7h 3
Transcription factor IIA (TFIIA), beta-barrel domain
(b.56.1.1)
1nvp 1
C-terminal, Zn-finger domain of MutM-like DNA repair proteins
(g.39.1.8)
1l2c 1
© NPIDB team 2003 - 2021

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