4DYO Hydrolase date Feb 29, 2012
title Crystal Structure Of Human Aspartyl Aminopeptidase (Dnpep) I With Aspartic Acid Hydroxamate
authors A.Chaikuad, E.Pilka, M.Vollmar, T.Krojer, J.R.C.Muniz, F.Von Delf C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, K.L.Kavanagh U.Oppermann, Structural Genomics Consortium (Sgc)
compound source
Molecule: Aspartyl Aminopeptidase
Chain: A
Fragment: See Remark 999
Synonym: Dnpep
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aspep, Dap, Dnpep
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-R3-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Cthf
symmetry Space Group: F 4 3 2
R_factor 0.155 R_Free 0.195
length a length b length c angle alpha angle beta angle gamma
244.595 244.595 244.595 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand GOL, MG, SD4, ZN enzyme Hydrolase E.C. BRENDA
note 4DYO supersedes 3L6S

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] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (4dyo.pdb1.gz) 1826 Kb
  • Biological Unit Coordinates (4dyo.pdb2.gz) 306 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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4DYO, from MSDmotif at EBI
  • Fold representative 4dyo from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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