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
DNA_pol_B_palm
(PF14792.5)
4ub3 4ub1 4ub2 4ymn 4ubc 4ubb 5bpc 5bom 4ub4 4yn4 5bol 4ymm 2fmq 5ugo 5tb9 5tbc 1bpz 5u2s 5u8h 5ugn 5ugp 5tb8 4m9h 1tva 3isc 5eoz 3isb 1bpx 5hhi 3c2m 3c2l 2p66 5wnz 4uaz 4gxi 4m9g 4m9n 4mf2 4mf8 4mfa 4mfc 4mff 4nln 4ny8 4o5c 4m2y 4pgq 4klu 4kld 4kle 4klf 4klh 4kli 4kll 4klo 4klg 4klq 4kls 4o5e 4uay 4rpy 4rq3 4rpz 4rq0 4rq1 4rq2 4rq4 4rq5 4rq6 4rq8 4tur 4tus 4uaw 4rpx 4pgx 4r63 4php 4ppx 4p2h 3rje 4phe 81
RVT_connect
(PF06815.12)
5txn 5hro 5j2p 5i3u 5i42 5d3g 5j2n 5txl 5j2m 5xn2 5txp 5xn1 5txm 5hlf 5j2q 5hp1 5xn0 5txo 4r5p 1r0a 1t03 3v6d 3kk1 3klh 3klg 3klf 3kk2 3kjv 1n6q 1n5y 1j5o 3v81 44
CENP-T_C
(PF15511.5)
1p3f 1p3b 3azm 1p3g 5cpk 3w97 3w99 3x1u 3azi 3aze 4z5t 1p3i 1p3p 21
Histone
(PF00125.23)
3x1s 3aze 2nqb 3c1c 5cpi 4ym6 1id3 1p3f 8
TFIIA
(PF03153.12)
5fz5 5iyc 5fyw 1rm1 1nvp 5fur 5iy8 7
DNA_pol_B
(PF00136.20)
3rma 3taf 2p5g 3rmd 4khy 2dtu 6
RHD_dimer
(PF16179.4)
1owr 3gut 1ram 2o61 1gji 1p7h 6
IMS_C
(PF11799.7)
4qwb 3in5 3pzp 2w7o 2v9w 5
Transposase_1
(PF01359.17)
4u7b 3hos 5hoo 3hot 8
HIN
(PF02760.14)
3rn5 3rn2 4l5r 4lnq 6
MutS_III
(PF05192.17)
3thy 3thw 3thx 1nne 5
Cas_Cas1
(PF01867.15)
5ds6 5wfe 5dlj 4
IMS
(PF00817.19)
2imw 4ir9 4r8u 3
DNA_pol_B_thumb
(PF14791.5)
2fmq 5wny 5tb9 3
IN_DBD_C
(PF00552.20)
5u1c 5ejk 3
MBD
(PF01429.18)
3c2i 5bt2 2
RAG2
(PF03089.13)
3jby 2
MutS_IV
(PF05190.17)
1nne 2
Tudor-knot
(PF11717.7)
3oa6 2
XPG_I
(PF00867.17)
5kse 1
DNA_ligase_A_M
(PF01068.20)
2q2t 1
Hjc
(PF01870.17)
2wiw 1
DNA_ligase_OB
(PF03120.15)
2owo 1
Rad4
(PF03835.14)
2qsg 1
DNA_ligase_A_C
(PF04679.14)
1x9n 1
Mu-transpos_C
(PF09299.10)
4fcy 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 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 - 2019

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