1pdn_C : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS (PROTEIN PRD PAIRED)
reference	Rould et al. 'Cell(Cambridge,Mass.)' 80 639 1995
source	Drosophila melanogaster
experiment	X-ray (resolution=2.50, R-factor=0.234)
structural superfamily	Homeodomain-like;
sequence family	'Paired box' domain;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1pdn_C interface=13,45,46,48,50,51,67,70, qgrvnqlggvfiNgrplpnnirlkivemaadgirpcvisrqlrvSHgCvSKilnryqetgsirpgvIggSkpriatpeienrieeykrsspgmfsweirekliregvcdrstapsvsaisrlv
interface signature	NSHCSKIS

Estimated binding specificities ?

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# IC=3.799 IC/col=0.543 n_of_columns=7

specificity:

A |   8  24   8  24  69   0   0
C |  69  24  11  24  11  87   0
G |  11  24   8  24   8   9  96
T |   8  24  69  24   8   0   0

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Dendrogram of similar interfaces ?

matrix format

  
  NG----STHG--CTSTKG----ITSA   L               +-----------------1pdn_C    
                                       +-------2 
  --KA------VT--KGDCRGTA----   L       !       !                 +1w0u_A    
                                     +-3       +-----------------1 
  --RT----RCET----SAQAKT----   L     ! !                         +6qec_A    
                                   +-4 ! 
  RT--HGSGRGHG--RT----------   L   ! ! +-------------------------1tc3_C    
                                 --5 ! 
  --RT----STVTMCKGDCRGTA----   L   ! +--------------------------1iv6_A    
                                   ! 
  --RA----RCET----SAQAKG----   L   +---------------------------5lxu_A

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updated Sun Aug 3 05:51:11 2025