4OJX Hydrolase date Jan 21, 2014
title Crystal Structure Of Yeast Phosphodiesterase-1 In Complex Wi
authors Y.Tian, W.Cui, M.Huang, H.Robinson, Y.Wan, Y.Wang, H.Ke
compound source
Molecule: 3',5'-Cyclic-Nucleotide Phosphodiesterase 1
Chain: A
Synonym: Pdease 1, 3':5'-Cnp, Low-Affinity Camp Phosphodies
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Pde1, Ygl248w, Nrb369
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: C 2 2 21
R_factor 0.168 R_Free 0.179
length a length b length c angle alpha angle beta angle gamma
73.674 85.162 130.836 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.31 Å
ligand G, MPD, ZN enzyme Hydrolase E.C. BRENDA

Primary referenceDual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate., Tian Y, Cui W, Huang M, Robinson H, Wan Y, Wang Y, Ke H, Biochemistry. 2014 Aug 5;53(30):4938-45. doi: 10.1021/bi500406h. Epub 2014 Jul, 22. PMID:25050706
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (4ojx.pdb1.gz) 253 Kb
  • LPC: Ligand-Protein Contacts for 4OJX
  • CSU: Contacts of Structural Units for 4OJX
  • Structure Factors (1826 Kb)
  • Retrieve 4OJX in mmCIF format [Save to disk]
  • Re-refined 4ojx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OJX 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 4OJX
  • 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 4OJX, from MSDmotif at EBI
  • Fold representative 4ojx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ojx_A] [4ojx]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4OJX
  • Community annotation for 4OJX at PDBWiki (http://pdbwiki.org)

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