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(-) Description

Title :  INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER
 
Authors :  L. Malinina, M. Soler-Lopez, J. Aymami, J. A. Subirana
Date :  25 Oct 00  (Deposition) - 16 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Biol. Unit 5:  I,J  (1x)
Biol. Unit 6:  K,L,M  (1x)
Keywords :  X-Ray Structure, Dna, Drug-Peptide Adduct, Intercalation, Mg+2 Ions (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Malinina, M. Soler-Lopez, J. Aymami, J. A. Subirana
Intercalation Of An Acridine-Peptide Drug In An Aa/Tt Base Step In The Crystal Structure Of [D(Cgcgaattcgcg)](2) With Six Duplexes And Seven Mg(2+) Ions In The Asymmetric Unit.
Biochemistry V. 41 9341 2002
PubMed-ID: 12135355  |  Reference-DOI: 10.1021/BI020135C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
    ChainsA, B, C, D, E, F, G, H, I, J, K, L
    EngineeredYES
    SyntheticYES
 
Molecule 2 - N(ALPHA)-(9-ACRIDINOYL)-TETRAARGININE-AMIDE
    ChainsM
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678910111213
Asymmetric Unit ABCDEFGHIJKLM
Biological Unit 1 (1x)AB           
Biological Unit 2 (1x)  CD         
Biological Unit 3 (1x)    EF       
Biological Unit 4 (1x)      GH     
Biological Unit 5 (1x)        IJ   
Biological Unit 6 (1x)          KLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
19AC1Mod. Amino Acid9-ACRIDINECARBONYL
2MG7Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
19AC-1Mod. Amino Acid9-ACRIDINECARBONYL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
19AC-1Mod. Amino Acid9-ACRIDINECARBONYL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
19AC-1Mod. Amino Acid9-ACRIDINECARBONYL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
19AC-1Mod. Amino Acid9-ACRIDINECARBONYL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
19AC-1Mod. Amino Acid9-ACRIDINECARBONYL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
19AC1Mod. Amino Acid9-ACRIDINECARBONYL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1not definedDG G:410 , HOH G:868 , HOH G:869 , HOH G:870 , HOH G:871 , HOH G:872 , HOH G:873
2AC2not definedHOH I:874 , HOH I:879 , HOH J:875 , HOH J:876 , HOH J:877 , HOH J:878
3AC3not definedDT B:120 , HOH B:880 , HOH B:881 , HOH B:882 , HOH B:884 , HOH B:885
4AC4not definedDG L:614 , HOH L:886 , HOH L:887 , HOH L:888 , HOH L:889 , HOH L:890
5AC5not definedDG K:602 , HOH K:892 , HOH K:893 , HOH K:894 , HOH K:895 , HOH K:896
6AC6not definedHOH A:898 , HOH A:901 , HOH A:903 , HOH B:899 , HOH B:900 , HOH B:902
7AC7not definedHOH K:905 , HOH K:907 , HOH K:908 , HOH L:904 , HOH L:906 , HOH L:909

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G3X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G3X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G3X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G3X)

(-) Exons   (0, 0)

(no "Exon" information available for 1G3X)

(-) 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:DNA  Length:12
                                            
                 1g3x A 101 CGCGAATTCGCG 112
                                   110  

Chain B from PDB  Type:DNA  Length:12
                                            
                 1g3x B 113 CGCGAATTCGCG 124
                                   122  

Chain C from PDB  Type:DNA  Length:12
                                            
                 1g3x C 201 CGCGAATTCGCG 212
                                   210  

Chain D from PDB  Type:DNA  Length:12
                                            
                 1g3x D 213 CGCGAATTCGCG 224
                                   222  

Chain E from PDB  Type:DNA  Length:12
                                            
                 1g3x E 301 CGCGAATTCGCG 312
                                   310  

Chain F from PDB  Type:DNA  Length:12
                                            
                 1g3x F 313 CGCGAATTCGCG 324
                                   322  

Chain G from PDB  Type:DNA  Length:11
                                           
                 1g3x G 402 GCGAATTCGCG 412
                                   411 

Chain H from PDB  Type:DNA  Length:12
                                            
                 1g3x H 413 CGCGAATTCGCG 424
                                   422  

Chain I from PDB  Type:DNA  Length:12
                                            
                 1g3x I 501 CGCGAATTCGCG 512
                                   510  

Chain J from PDB  Type:DNA  Length:12
                                            
                 1g3x J 513 CGCGAATTCGCG 524
                                   522  

Chain K from PDB  Type:DNA  Length:12
                                            
                 1g3x K 601 CGCGAATTCGCG 612
                                   610  

Chain L from PDB  Type:DNA  Length:12
                                            
                 1g3x L 613 CGCGAATTCGCG 624
                                   622  

Chain M from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1g3x M 700 xRRRR 704
                            |    
                          700-9AC

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 1G3X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1G3X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G3X)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1G3X)

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