3mx9_A : 3D-footprint complex

structure name	MOLECULAR BASIS OF ENGINEERED MEGANUCLEASE TARGETING OF THE ENDOGENOUS HUMAN RAG1 LOCUS (Protein scV3V2G19S)
reference	Subramanian et al. 'Nucleic 39 729 2011
source	Chlamydomonas reinhardtii
experiment	X-ray (resolution=2.60, R-factor=0.184)
structural superfamily	Homing endonucleases;
sequence family	LAGLIDADG endonuclease;
multimeric complexes	2vbj_AB 2vbo_AB 2xe0_AB 3mxb_AB 3mxb_RS 6fb0_AB 6fb5_AB
reference complex	2vbo_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3mx9_A interface=21,23,25,31,37,39,43,45,65,67,72,74,167,169,171,173,175,177,178,183,189,191,213,215,218,220,222,224,285, ntkynkefllylagfvdgdgSiIaQinpnqSskfkhRlRltfYvTqktqrrwfldklvdeigvgYvRdsgsVsQyvlseikplhnfltqlqpflklkqkqanlvlkiieqlpsakespdkflevctwvdqiaalndsktrkttsetvrasnkefllylagfvdsdgSiIaQiKpRqSNkfkhQlsltfAvTqktqrrwfldklvdeigvgyvYdSgsVsDyRlSeikplhnfltqlqpflklkqkqanlvlkiieqlpsakespdkflevctwvdqiaalndskTrkttsetvravld
interface signature	SIQSRRYTYRVQSIQKRSNQATYSVDRST

Estimated binding specificities ?

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# IC=23.591 IC/col=0.983 n_of_columns=24

specificity:

A |   2   0   0   5  24   0   0   0  96   2  24   0  87   5   5   0   0  96   2   0   0  81  24  87
C |   2   0   0  10  24  96   0  96   0   2  24   3   2  87  78   0  96   0   2  96  96   8  24   2
G |   2   0  96   5  24   0   0   0   0  87  24   0   5   2   8   0   0   0  76   0   0   2  24   5
T |  90  96   0  76  24   0  96   0   0   5  24  93   2   2   5  96   0   0  16   0   0   5  24   2

scan!

Dendrogram of similar interfaces ?

matrix format

  
  STITQA----ST--RGRGYCTCYC--RG------VCQT--------STITQAKGRGSTNTQT--ATTC--YTSC--VCDTRGSTTG   L                   +------3mx9_A    
                                                                                                 +-------------2 
  SGMGRGRG--KTYALTVT--TT--KT--SC----TA--RGEC------KGITKG--SGITQAICQATCECDTRG--WTYC--TC--   L     !             !     +5e67_A    
                                                                                               +-3             +-----1 
  ST--SC--------HTRTTTMT----LTNC----YA----YA----SAFCRGRG------RGQGECSC------RTWCQTRTEC--   L   ! !                   +7rcf_A    
                                                                                             --4 ! 
  STITQAKGRGSTNTQTSTATTC----YT--SC--VCDTRGSTKGTG----------------------------------------   L   ! +--------------------3mxb_B    
                                                                                               ! 
  CA--QGVTRTDCYA--RT--FG----RGRGNTDTMCEA------KG----------------------------------------   L   +----------------------5a78_B

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updated Thu Jan 8 22:20:47 2026