Web Server of Protein-DNA Complex Structure Analyzer1,2 Last updated on: Feb 20, 2013 |
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PDA Analysis Report for 1gtw (Protein-DNA Atom Contact Cutoff=4.8 Angstroms) |
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PDAgram |
HELIX 0 PROTEIN CHAIN ID (CONTACTING DNA BASE): AAAA*BBBB HELIX 0 CONTACT TYPE (PROTEIN-DNA BASE) : MMMMMMMMM HELIX 0 DNA CHAIN ID (UPPER STRAND) : DDDDDDDDDDDDDDDD HELIX 0 DNA SEQUENCE (UPPER STRAND) : 5' taggATTGCGCCAcat HELIX 0 BASE-PAIRING TYPE : ............... HELIX 0 DNA SEQUENCE (LOWER STRAND) : 3' tcctAACGCGGTGtaa HELIX 0 DNA CHAIN ID (LOWER STRAND) : CCCCCCCCCCCCCCCC HELIX 0 CONTACT TYPE (PROTEIN-DNA BASE) : MMMMMMMMM HELIX 0 PROTEIN CHAIN ID (CONTACTING DNA BASE): AAAA*BBBB HELIX 0 MDN: DC10:C A,F HELIX 0 MDN: DG9:C A,F HELIX 0 MDN: DC109:D A,B HELIX 0 MDN: DC8:C A,B HELIX 0 MDN: DC8:C A,E,F HELIX 1 PROTEIN CHAIN ID (CONTACTING DNA BASE): EEEE*FFFF HELIX 1 CONTACT TYPE (PROTEIN-DNA BASE) : MMMMMMMMM HELIX 1 DNA CHAIN ID (UPPER STRAND) : HHHHHHHHHHHHHHHH HELIX 1 DNA SEQUENCE (UPPER STRAND) : 5' taggATTGCGCCAcat HELIX 1 BASE-PAIRING TYPE : ............... HELIX 1 DNA SEQUENCE (LOWER STRAND) : 3' tcctAACGCGGTGtaa HELIX 1 DNA CHAIN ID (LOWER STRAND) : GGGGGGGGGGGGGGGG HELIX 1 CONTACT TYPE (PROTEIN-DNA BASE) : MMMMMMMMM HELIX 1 PROTEIN CHAIN ID (CONTACTING DNA BASE): EEEE*FFFF HELIX 1 MDN: DC10:G B,E HELIX 1 MDN: DG9:G B,E HELIX 1 MDN: DC109:H E,F HELIX 1 MDN: DC8:G E,F HELIX 1 MDN: DC8:G E,A,B |
PROTEIN |
Number of protein chains = 4 Length of protein chains (in aa) = 66 ~ 68 Protein Chains in contact with DNA = |
DNA |
Number of double-stranded DNA = 2 Lengths of double-stranded DNAs (in bp) = 17 ~ 17 GC content of double-stranded DNAs = 0.514 Number of cracks4 in double-stranded DNAs = 0 |
PROTEIN-DNA Interactions |
Average major/minor groove contact ratio = 1.000 Average base/backbone contact ratio = 0.514 Average number of DNA bases whose major groove is in contact with protein = 18 Average number of DNA bases whose minor groove is in contact with protein = 0 Average number of DNA bases which are in contact with protein = 18 Average number of nucleotides whose backbone is in contact with protein = 17 Number of double-stranded DNA sides that are blocked by protein = 0.47 |
OTHER INFORMATION |
Deposition date = 2002-01-22 Resolution = 1.85 Number of protein-DNA binding units = 2 |
| 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 |