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(-) Description

Title :  CRYSTAL STRUCTURE OF A PARTLY SELF-COMPLEMENTARY PEPTIDE NUCLEIC ACID (PNA) OLIGOMER SHOWING A DUPLEX-TRIPLEX NETWORK
 
Authors :  B. Petersson, B. B. Nielsen, H. Rasmussen, I. K. Larsen, M. Gajhede, P. E J. S. Kastrup
Date :  23 Sep 04  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Pna, Peptide Nucleic Acid, Partly Self-Complementary, Duplex-Triplex Complex, Right-Handed, Left-Handed (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Petersson, B. B. Nielsen, H. Rasmussen, I. K. Larsen, M. Gajhede, P. E. Nielsen, J. S. Kastrup
Crystal Structure Of A Partly Self-Complementary Peptide Nucleic Acid (Pna) Oligomer Showing A Duplex-Triplex Networ
J. Am. Chem. Soc. V. 127 1424 2005
PubMed-ID: 15686374  |  Reference-DOI: 10.1021/JA0458726
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE NUCLEIC ACID, (H- P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)
    Chains: A, B
    Engineered: YES
    Synonym: PNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1APN6Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
3GPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
4TPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1APN6Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
3GPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
4TPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1APN6Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
3GPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
4TPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE

(-) Sites  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1xj9 A 103 xxxxxxxxK 111
                            |||||||| 
                            |||||||| 
                          103-APN||| 
                           104-GPN|| 
                            105-APN| 
                             106-TPN 
                              107-CPN
                               108-APN
                                109-CPN
                                 110-TPN


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1xj9 B 203 xxxxxxxxK 211
                            |||||||| 
                            |||||||| 
                          203-APN||| 
                           204-GPN|| 
                            205-APN| 
                             206-TPN 
                              207-CPN
                               208-APN
                                209-CPN
                                 210-TPN
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

176d PEPTIDE NUCLEIC ACID COMPLEXED WITH RNA
1nr8 A D-LYSINE-BASED CHIRAL PEPTIDE NUCLEIC ACID/DNA DUPLEX
1pdt PEPTIDE NUCLEIC ACID COMPLEXED WITH DNA
1pnn PEPTIDE NUCLEIC ACID/DNA TRIPLEX
1pup PEPTIDE NUCLEIC ACID DUPLEX
1rru PEPTIDE NUCLEIC ACID WITH L-LYS IN C-TERMINUS