1JDG Dna date Jun 13, 2001
title Solution Structure Of A Trans-Opened (10s)-Da Adduct Of (+)- 10r)-7,8-Dihydroxy-9,10-Epoxy-7,8,9,10-Tetrahydrobenzo[A]Py Fully Complementary Dna Duplex
authors P.Pradhan, S.Tirumala, X.Liu, J.M.Sayer, D.M.Jerina, H.J.C.Yeh
compound source
Molecule: 5'-D(Cpgpgptpcp(Bpa)Apcpgpapgpg)-3'
Chain: A
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Cpcptpcpgptpgpapcpcpg)-3'
Chain: B
Engineered: Yes

Synthetic: Yes
methodSolution NMR
ligand BPA enzyme
Primary referenceSolution structure of a trans-opened (10S)-dA adduct of (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyr ene in a fully complementary DNA duplex: evidence for a major syn conformation., Pradhan P, Tirumala S, Liu X, Sayer JM, Jerina DM, Yeh HJ, Biochemistry 2001 May 22;40(20):5870-81. PMID:11352722
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (15 Kb) [Save to disk]
  • Biological Unit Coordinates (1jdg.pdb1.gz) 12 Kb
  • LPC: Ligand-Protein Contacts for 1JDG
  • CSU: Contacts of Structural Units for 1JDG
  • Original NMR restraints for 1JDG from PDB
  • Retrieve 1JDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JDG from S2C, [Save to disk]
  • View 1JDG in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1JDG
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1JDG, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1jdg_B] [1jdg_A] [1jdg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 1JDG
  • Community annotation for 1JDG at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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