3I8V Hydrolase date Jul 10, 2009
title Crystal Structure Of Human Pde4a With 4-(3-Butoxy-4-Methoxyp Methyl-2-Imidazolidone
authors R.K.Y.Cheng, L.Crawley, J.Barker, M.Wood, B.Felicetti, M.Whittake
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4a
Chain: A, B
Fragment: Catalytic Domain
Synonym: Dpde2, Pde46
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde4a, Dpde2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28(A)
symmetry Space Group: P 41 21 2
R_factor 0.187 R_Free 0.222
length a length b length c angle alpha angle beta angle gamma
105.406 105.406 165.252 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand 0MO, CO, CSS, GOL, MG, ZN BindingDB enzyme Hydrolase E.C. BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (3i8v.pdb1.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 3I8V
  • CSU: Contacts of Structural Units for 3I8V
  • Likely Quarternary Molecular Structure file(s) for 3I8V
  • Structure Factors (664 Kb)
  • Retrieve 3I8V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I8V from S2C, [Save to disk]
  • Re-refined 3i8v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3I8V 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 3I8V
  • 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 3I8V, from MSDmotif at EBI
  • Fold representative 3i8v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i8v_A] [3i8v] [3i8v_B]
  • SWISS-PROT database: [P27815]
  • Domain organization of [PDE4A_HUMAN] by SWISSPFAM
  • Domain found in 3I8V: [HDc ] by SMART
  • Other resources with information on 3I8V
  • Community annotation for 3I8V 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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