3bam_A : 3D-footprint complex

structure name	RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX) (PROTEIN RESTRICTION ENDONUCLEASE BAMHI)
reference	Aggarwal et al.
source	Bacillus amyloliquefaciens
experiment	X-ray (resolution=1.80, R-factor=0.226)
structural superfamily	Restriction endonuclease-like;
sequence family	Restriction endonuclease BamHI;
multimeric complexes	1bhm_AB 1esg_AB 2bam_AB 3bam_AB
redundant complexes	1bhm_A 1esg_A 2bam_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3bam_A interface=116,122,153,154,155,156,196,198, mevekefitdeakellskdkliqqaynevktsicspiwpatsktftinntekncngvvpikelcytlledtynwyrekpldilklekkkggpidvykefienselkrvgmefetgNissahRsmnklllglkhgeidlaiilmpikqlayylTDRVtnfeelepyfeltegqpfifigfnaeaynsnvplipkgsDgMskrsikkw
interface signature	NRTDRVDM

Estimated binding specificities ?

readout + contact

# IC=6.693 IC/col=0.956 n_of_columns=7

specificity:

A |   0   0   0  96  19   0   9
C |   9   0   0   0  10  96  48
G |   0  96  96   0  19   0  20
T |  87   0   0   0  48   0  19

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: BAMHI
GGATCC	PubMed	3bam_A(9.60e-06), 1bhm_AB(4.43e-09), 2bam_AB(4.43e-09), ... (total=4)
GATCC	PubMed	3bam_A(1.15e-06), 1bhm_AB(1.91e-06), 2bam_AB(1.91e-06), ... (total=5)
CCGGATCCGG	PubMed	3bam_A(8.95e-04), 1bhm_AB(1.41e-05), 2bam_AB(1.41e-05), ... (total=4)
TATGGATCCATA	PubMed	3bam_A(6.47e-06), 1bhm_AB(6.26e-08), 1esg_AB(7.87e-03), ... (total=6)
TGATCC	PubMed	3bam_A(9.60e-06), 1bhm_AB(2.02e-05), 2bam_AB(2.02e-05), ... (total=4)
GACGGATCCGTC	PubMed	3bam_A(2.06e-03), 1bhm_AB(5.04e-05), 2bam_AB(5.04e-05), ... (total=4)
ATGGCGGATCCGC	PubMed	3bam_A(2.59e-03), 1bhm_AB(7.22e-05), 2bam_AB(7.22e-05), ... (total=4)
GGATCCGGATCC	PubMed	3bam_A(2.06e-03), 1bhm_AB(5.04e-05), 2bam_AB(5.04e-05), ... (total=4)
ATGAATCCATA	PubMed	3bam_A(1.46e-03), 1bhm_AB(2.16e-04), 1esg_AB(5.48e-03), ... (total=7)

Dendrogram of similar interfaces ?

matrix format

  
  KA----------------NG------RGKT--YTTTDCRGVT----DGMT   L                              +----3bam_A    
                                                                      +---------------1 
  --------RT--------NG------RGRTYT--TTDCRG----------   L           +--2               +----3odh_F    
                                                                   !  ! 
  ----------------SANTYA--FG--------STNTSAST--------   L         +-3  +--------------------1dfm_A    
                                                                 ! ! 
  ------------------KGYT--------------SC------------   L       +-4 +-----------------------2p0j_A    
                                                               ! ! 
  ----------RC------------RT------------------------   L     +-5 +-------------------------4dav_B    
                                                             ! ! 
  --TG--KC------TC--QGLG--MC----------------DCKA----   L   +-6 +---------------------------1wte_A    
                                                           ! ! 
  ----AA------RAKG--RGECRG--------------------------   L --7 +----------------------------3bm3_A    
                                                           ! 
  ----------------RG--------------------------------       +----------------------------5dff_A

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updated Tue Dec 19 07:10:53 2023