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(-) Description

Title :  CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID DUPLEX (BT-PNA) CONTAINING A BICYCLIC ANALOGUE OF THYMINE
 
Authors :  A. B. Eldrup, B. B. Nielsen, G. Haaima, H. Rasmussen, J. S. Kastrup, C. Christensen, P. E. Nielsen
Date :  26 Jan 01  (Deposition) - 26 Jul 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Peptide Nucleic Acid, Double Helix, Nucleobase Analogue, P-Form Helix, Left-Handed, Right-Handed (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Eldrup, B. B. Nielsen, G. Haaima, H. Rasmussen, J. S. Kastrup, C. Christensen, P. E. Nielsen
1, 8-Naphthyridin-2(1H)-Ones. Novel Bicyclic And Tricyclic Analogues Of Thymine In Peptide Nucleic Acids (Pnas)
Eur. J. Org. Chem. V. 9 1781 2001
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE NUCLEIC ACID
    Chains: A, B, C, D
    Engineered: YES
    Other Details: SYNTHESIZED AS DESCRIBED IN THE PRIMARY REFERENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 28)

Asymmetric Unit (6, 28)
No.NameCountTypeFull Name
1APN8Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
3GPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
4NH24Mod. Amino AcidAMINO GROUP
5OPN4Mod. Amino Acid{(2-AMINO-ETHYL)-[2-(2-OXO-1,2-DIHYDRO-[1,8]NAPHTHYRIDIN-3-YL)-ACETYL]-AMINO}-ACETIC ACID
6TPN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 1 (6, 14)
No.NameCountTypeFull Name
1APN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
3GPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
4NH22Mod. Amino AcidAMINO GROUP
5OPN2Mod. Amino Acid{(2-AMINO-ETHYL)-[2-(2-OXO-1,2-DIHYDRO-[1,8]NAPHTHYRIDIN-3-YL)-ACETYL]-AMINO}-ACETIC ACID
6TPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
Biological Unit 2 (6, 14)
No.NameCountTypeFull Name
1APN4Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
3GPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
4NH22Mod. Amino AcidAMINO GROUP
5OPN2Mod. Amino Acid{(2-AMINO-ETHYL)-[2-(2-OXO-1,2-DIHYDRO-[1,8]NAPHTHYRIDIN-3-YL)-ACETYL]-AMINO}-ACETIC ACID
6TPN2Mod. Amino Acid2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:7BINDING SITE FOR RESIDUE NH2 A 8
2AC2SOFTWARELYS B:15BINDING SITE FOR RESIDUE NH2 B 16
3AC3SOFTWARELYS C:23BINDING SITE FOR RESIDUE NH2 C 24
4AC4SOFTWARECPN D:30 , LYS D:31BINDING SITE FOR RESIDUE NH2 D 32

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HZS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HZS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HZS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HZS)

(-) Exons   (0, 0)

(no "Exon" information available for 1HZS)

(-) 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:8
                                       
               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
                  1hzs A  1 xxxxxxKx  8
                            |||||| |
                            |||||| |
                            1-GPN| |
                             2-OPN |
                              3-APN|
                               4-TPN
                                5-APN
                                 6-CPN
                                   8-NH2


Chain B from PDB  Type:PROTEIN  Length:8
                                       
               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
                  1hzs B  9 xxxxxxKx 16
                            |||||| |
                            |||||| |
                            9-GPN| |
                            10-OPN |
                             11-APN|
                              12-TPN
                               13-APN
                                14-CPN
                                  16-NH2


Chain C from PDB  Type:PROTEIN  Length:8
                                       
               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
                  1hzs C 17 xxxxxxKx 24
                            |||||| |
                            |||||| |
                           17-GPN| |
                            18-OPN |
                             19-APN|
                              20-TPN
                               21-APN
                                22-CPN
                                  24-NH2


Chain D from PDB  Type:PROTEIN  Length:8
                                       
               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
                  1hzs D 25 xxxxxxKx 32
                            |||||| |
                            |||||| |
                           25-GPN| |
                            26-OPN |
                             27-APN|
                              28-TPN
                               29-APN
                                30-CPN
                                  32-NH2
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1HZS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1HZS)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

176d PEPTIDE NUCLEIC ACID COMPLEXED WITH RNA
1pdt PEPTIDE NUCLEIC ACID COMPLEXED WITH DNA
1pnn PEPTIDE NUCLEIC ACID/DNA TRIPLEX
1pup PEPTIDE NUCLEIC ACID DUPLEX