2R5D Structure of the gp41 N-trimer in complex with the HIV entry inhibitor PIE7 date
authors VanDemark, A.P., Welch, B., Heroux, A., Hill, C.P., Kay, M.S.
compound source
symmetry
R_factor
R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.66
ligand ACE, DAL, DAS, DCY, DGL, DGN, DLE, DLY, DPR, DTR, DTY, EPE, GOL, NH2, SO4 enzyme
Primary referencePotent D-peptide inhibitors of HIV-1 entry., Welch BD, Vandemark AP, Heroux A, Hill CP, Kay MS, Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16828-33. Epub 2007 Oct 17. PMID:17942675
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (2r5d.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 2R5D
  • CSU: Contacts of Structural Units for 2R5D
  • Likely Quarternary Molecular Structure file(s) for 2R5D
  • Structure Factors (167 Kb)
  • Retrieve 2R5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R5D from S2C, [Save to disk]
  • Re-refined 2r5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2R5D 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 2R5D
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2R5D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r5d_H] [2r5d_C] [2r5d_A] [2r5d_K] [2r5d] [2r5d_L] [2r5d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2R5D
  • Community annotation for 2R5D 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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