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(-) Description

Title :  SOLUTION STRUCTURE OF A 2:1C2-(2-NAPHTHYL)PYRROLO[2,1-C][1, 4]BENZODIAZEPINE (PBD) DNA ADDUCT: MOLECULAR BASIS FOR UNEXPECTEDLY HIGH DNA HELIX STABILIZATION.
 
Authors :  D. Antonow, T. Barata, T. C. Jenkins, G. N. Parkinson, P. W. Howard, D. E. M. Zloh
Date :  13 Jun 08  (Deposition) - 28 Oct 08  (Release) - 11 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Pyrrolo[2, 1-C][1, 4]Benzodiazepine, Pbd, Dna Adduct, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Antonow, T. Barata, T. C. Jenkins, G. N. Parkinson, P. W. Howard, D. E. Thurston, M. Zloh
Solution Structure Of A 2:1 C2-(2-Naphthyl) Pyrrolo[2, 1-C][1, 4]Benzodiazepine Dna Adduct: Molecular Basis For Unexpectedly High Dna Helix Stabilization.
Biochemistry V. 47 11818 2008
PubMed-ID: 18925745  |  Reference-DOI: 10.1021/BI801225Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*D T)-3'
    Chains: A, B
    Engineered: YES
    Other Details: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE DUPLEX WAS FORMED BY ANNEALING IN PHOSPHATE BUFFER.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1PZD2Ligand/Ion(11AS)-7,8-DIMETHOXY-2-NAPHTHALEN-2-YL-1,10,11,11A-TETRAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:11 , DA A:12 , DT A:13 , DT A:14 , DC B:24 , DT B:25 , DT B:26 , DT B:27BINDING SITE FOR RESIDUE PZD A 101
2AC2SOFTWAREDT A:3 , DC A:4 , DT A:5 , DT A:6 , DT A:7 , DG B:31 , DA B:32 , DT B:33 , DT B:34BINDING SITE FOR RESIDUE PZD B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K4L)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:DNA  Length:14
                                             
                  2k4l A  1 AATCTTTAAAGATT 14
                                    10    


Chain B from PDB  Type:DNA  Length:14
                                             
                  2k4l B 21 AATCTTTAAAGATT 34
                                    30
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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NMR Structure(hide GO term definitions)
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