4HQX CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4) date
authors Davies, D.R., Edwards, T.E., Janjic, N., Gelinas, A.D., Zhang, C., Jarvis, T.C.
compound source
symmetry
R_factor
R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.30
ligand 18M, 18Q, A2M, DUZ, MG, NA, PE6, UBI, UPE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUnique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets., Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC, Proc Natl Acad Sci U S A. 2012 Nov 8. PMID:23139410
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (4hqx.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 4HQX
  • CSU: Contacts of Structural Units for 4HQX
  • Structure Factors (196 Kb)
  • Retrieve 4HQX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4HQX from S2C, [Save to disk]
  • Re-refined 4hqx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4HQX 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 4HQX
  • 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 4HQX, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4hqx_C] [4hqx] [4hqx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4HQX: [PDGF ] by SMART
    • Other resources with information on 4HQX
  • Community annotation for 4HQX at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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