1per_L : 3D-footprint complex

structure name	THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON- CONSENSUS HALF-SITES (PROTEIN 434 REPRESSOR)
reference	Harrison et al.
source	PHAGE 434
experiment	X-ray (resolution=2.50, R-factor=0.187)
structural superfamily	lambda repressor-like DNA-binding domains;
sequence family	Helixturnhelix;
multimeric complexes	1per_LR 1rpe_LR 2or1_LR
redundant complexes	1rpe_R 2or1_R
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1per_L interface=17,27,28,29,30,32,33,38,43, sissrvkskriqlglnQaelaqkvgtTQQSiEQlengKtkrpRflpelasalgvsvdwllngt
interface signature	QTQQSEQKR

Estimated binding specificities ?

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# IC=4.638 IC/col=0.928 n_of_columns=5

specificity:

A |   0  16   0   0  48
C |   0  16   0   0  16
G |   0   0  96   0  16
T |  96  64   0  96  16

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: 434 REPRESSOR
CATACAAGAAAGNNNNNNTTT	PubMed	1per_L(8.44e-05), 2or1_L(1.40e-05)
ACAAGA	PubMed	1per_L(4.51e-04), 2or1_LR(3.69e-04), 2or1_L(3.89e-05)
ACAGTTTTCTTGT	PubMed	1per_L(1.02e-02), 2or1_LR(1.46e-03), 1rpe_L(9.94e-03), ... (total=4)
ACAAAACTTTCTTGT	PubMed	1rpe_LR(1.00e-02), 2or1_LR(1.46e-04), 2or1_L(8.52e-04)

Dendrogram of similar interfaces ?

matrix format

  
  QT--STNTVTATSTQTRTETTT   L                              +--2r1j_L    
                                                     +----1 
  --AT--QAAT--SA--------       +---------------------2    +--4z5h_A    
                               !                     ! 
  ----TTQA--LTSAET------   L --3                     +-------2o4a_A    
                               ! 
  ----SGQATT----RG------   L   +-----------------------------1o4x_A

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updated Fri Sep 13 15:55:46 2024