5od6_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF SMAD3-MH1 BOUND TO THE GGCGC SITE. (Mothers against decapentaplegic homolog 3)
reference	Kaczmarska et al. 'Nat 8 2070 2017
source	Homo sapiens
experiment	X-ray (resolution=2.00, R-factor=0.197)
structural superfamily	SMAD MH1 domain;
sequence family	MH1 domain;
multimeric complexes	1mhd_AB 1ozj_AB
redundant complexes	1mhd_B 1ozj_B 5odg_A 6zmn_B
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5od6_A interface=63,65,67,72, mivkrllgwkkgeqngqeekwcekavkslvkklkktgqldelekaittqnvntkcitiprslDgRlQvshrKglphviycrlwrwpdlhshhelramelcefafnmkkdevcvnpyhyqrvetpv
interface signature	DRQK

Estimated binding specificities ?

readout + contact

# IC=2.248 IC/col=0.562 n_of_columns=4

specificity:

A |   6   9   9   4
C |  77   7  57  82
G |   5  71  12   5
T |   8   9  18   5

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: SMAD3
GTCTAGAC	PubMed	1mhd_AB(6.56e-08), 1ozj_AB(1.10e-13), 1mhd_B(1.79e-05), ... (total=4)
CAGACA	PubMed	1mhd_AB(7.82e-05), 1ozj_AB(4.08e-05), 1mhd_B(1.13e-03), ... (total=4)
TGCCAGACA	PubMed	1mhd_AB(8.10e-03), 1ozj_AB(1.67e-04), 1mhd_B(1.03e-02), ... (total=4)
TGTGTATT	PubMed	1mhd_AB(3.04e-05), 1ozj_AB(6.73e-03)

Dendrogram of similar interfaces ?

matrix format

  
  --RGQC--KG   L            +5od6_A    
                          +-1 
  DCRGQC--KG   L   +------4 +6tbz_A    
                   !      ! 
  --RGQA--KA   L   !      +-6h3r_A    
                 --6 
  DCRGQC--KG   L   !      +-6fzt_A    
                   !      ! 
  --RGQAHTKG   L   +------5   +5x6g_A    
                          ! +-2 
  --RGQA--KG   L          +-3 +3kmp_A    
                            ! 
  DCRGQC--KG   L            +6zmn_B

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updated Fri Sep 13 20:17:12 2024