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(-) Description

Title :  THE CRYSTAL STRUCTURE OF BERBERINE BOUND TO DNA D(CGTACG)
 
Authors :  M. Ferraroni, C. Bazzicalupi, P. Gratteri, A. R. Bilia
Date :  28 Jun 10  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Drug-Dna Complex, Double Helix, B-Dna, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ferraroni, C. Bazzicalupi, A. R. Bilia, P. Gratteri
X-Ray Diffraction Analyses Of The Natural Isoquinoline Alkaloids Berberine And Sanguinarine Complexed With Double Helix Dna D(Cgtacg)
Chem. Commun. (Camb. ) V. 47 4917 2011
PubMed-ID: 21431128  |  Reference-DOI: 10.1039/C1CC10971E

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*TP*AP*CP*G)-3'
    Chains: A, B, C, D
    Engineered: YES
    Other Details: SYNTHETIC DNA
    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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1BER1Ligand/IonBERBERINE
2CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BER-1Ligand/IonBERBERINE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BER1Ligand/IonBERBERINE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC A:5 , DG A:6 , DC B:7 , DG B:8 , DC C:5 , DG C:6 , DC D:7 , DG D:8BINDING SITE FOR RESIDUE BER C 7
2AC2SOFTWAREDG B:12 , DG D:12BINDING SITE FOR RESIDUE CA B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NP6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NP6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:6
                                     
                  3np6 A  1 CGTACG  6


Chain B from PDB  Type:DNA  Length:6
                                     
                  3np6 B  7 CGTACG 12


Chain C from PDB  Type:DNA  Length:6
                                     
                  3np6 C  1 CGTACG  6


Chain D from PDB  Type:DNA  Length:6
                                     
                  3np6 D  7 CGTACG 12
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3NP6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NP6)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3nx5