2HMD Dna date Jul 11, 2006
title Stereochemistry Modulates Stability Of Reduced Inter-Strand Links Arising From R- And S-Alpha-Methyl-Gamma-Oh-1,N2-Prop Deoxyguanine In The 5'-Cpg-3' Dna Sequence
authors Y.J.Cho, I.D.Kozekov, T.M.Harris, C.J.Rizzo, M.P.Stone
compound source
Molecule: Dna Dodecamer With Interstrand Cross-Link
Chain: A
Engineered: Yes
Other_details: G7 Of Chain A And B Linked
 Synthetic: Yes

Molecule: Dna Dodecamer With Interstrand Cross-Link
Chain: B
Engineered: Yes
Other_details: G7 Of Chain A And B Linked
Synthetic: Yes
methodSolution NMR
ligand 2EG enzyme
Primary referenceStereochemistry Modulates the Stability of Reduced Interstrand Cross-Links Arising from R- and S-alpha-CH(3)-gamma-OH-1,N(2)-Propano-2'-deoxyguanosine in the 5'-CpG-3' DNA Sequence., Cho YJ, Kozekov ID, Harris TM, Rizzo CJ, Stone MP, Biochemistry. 2007 Mar 13;46(10):2608-21. Epub 2007 Feb 17. PMID:17305317
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (17 Kb) [Save to disk]
  • Biological Unit Coordinates (2hmd.pdb1.gz) 13 Kb
  • LPC: Ligand-Protein Contacts for 2HMD
  • CSU: Contacts of Structural Units for 2HMD
  • Original NMR restraints for 2HMD from PDB
  • Retrieve 2HMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HMD from S2C, [Save to disk]
    • View 2HMD 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 2HMD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2HMD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hmd] [2hmd_B] [2hmd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2HMD
  • Community annotation for 2HMD 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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