4DYO Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid Hydroxamate date 2012-02-29
authors Chaikuad, A., Pilka, E., Vollmar, M., Krojer, T., Muniz, J.R.C., Delft, F.von., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Kavanagh, K.L., Oppermann, U., SGC, Structural.Genomics.Consortium.
compound source
symmetry
R_factor
R_Free 0.1947
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.20
ligand GOL, MG, SD4, ZN enzyme
note 4DYO supersedes 3L6S
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family., Chaikuad A, Pilka ES, Riso AD, Delft FV, Kavanagh KL, Venien-Bryan C, Oppermann U, Yue WW, BMC Struct Biol. 2012 Jun 21;12(1):14. PMID:22720794
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (4dyo.pdb1.gz) 1780 Kb
  • Biological Unit Coordinates (4dyo.pdb2.gz) 298 Kb
  • LPC: Ligand-Protein Contacts for 4DYO
  • CSU: Contacts of Structural Units for 4DYO
  • Structure Factors (521 Kb)
  • Retrieve 4DYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DYO from S2C, [Save to disk]
  • Re-refined 4dyo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DYO 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 4DYO
  • 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 4DYO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dyo] [4dyo_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4DYO
  • Community annotation for 4DYO at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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