Web Server of Protein-DNA Complex Structure Analyzer1,2
Last updated on: Feb 20, 2013

PDA Analysis Report for 1bgb (Protein-DNA Atom Contact Cutoff=4.8 Angstroms)
(Click Here for PDA analysis result for 1bgb in text)
PDA analysis







Legends Blue: major groove atoms in contact with protein
Red: minor groove atoms in contact with protein
Yellow: protein residues in contact with DNA bases

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HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):     BB***A*B  
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :     MMAMMMAm  
HELIX  0 DNA CHAIN ID (UPPER STRAND)           :    DDDDDDDDDD 
HELIX  0 DNA SEQUENCE (UPPER STRAND)           : 5' gGGATATCCc 
HELIX  0 BASE-PAIRING TYPE                     :    .......... 
HELIX  0 DNA SEQUENCE (LOWER STRAND)           : 3' ccCTATAGGgc
HELIX  0 DNA CHAIN ID (LOWER STRAND)           :    CCCCCCCCCCC
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :      MMMAAAM  
HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):      BB*B**A  
HELIX  0 MDN: DC810:C B,A
HELIX  0 MDN: DC809:C B,A
HELIX  0 MDN: DA905:D B,A
HELIX  0 MDN: DA807:C B,A
HELIX  0 MDN: DT906:D A,B
HELIX  0 MDN: DA907:D A,B
HELIX  0 MDN: DA805:C A,B
HELIX  0 MDN: DG804:C A,B
HELIX  0 MDN: DC909:D B,A
HELIX  0 MDN: DC909:D A,B
PROTEIN
Number of protein chains = 2
Length of protein chains (in aa) = 228 ~ 237
Protein Chains in contact with DNA =

DNA
Number of double-stranded DNA = 1
Lengths of double-stranded DNAs (in bp) = 11 ~ 11
GC content of double-stranded DNAs = 0.417
Number of cracks4 in double-stranded DNAs = 0

PROTEIN-DNA Interactions
Average major/minor groove contact ratio = 0.700
Average base/backbone contact ratio = 0.417
Average number of DNA bases whose major groove is in contact with protein = 14
Average number of DNA bases whose minor groove is in contact with protein = 6
Average number of DNA bases which are in contact with protein = 15
Average number of nucleotides whose backbone is in contact with protein = 21
Number of double-stranded DNA sides that are blocked by protein = 0.64

OTHER INFORMATION
Deposition date = 1998-05-28
Resolution = 2.00
Number of protein-DNA binding units = 1
1Kim R. and Guo, J-T. "PDA: an automatic and comprehensive analysis program for protein-DNA complex structures", BMC Genomics,10(Supple 1):S13, 2009
2This work is supported by the NSF CAREER award DBI-0844749
33DNA v1.5 reference: Xiang-Jun Lu & Wilma K. Olson (2003). Nucleic Acids. Res., 31(17), 5108-5121
4Severe deformation of a double-stranded DNA with a break in its backbone

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