3G4G Hydrolase date Feb 03, 2009
title Crystal Structure Of Human Phosphodiesterase 4d With Regulat And D155871
authors B.L.Staker
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d
Chain: A, B, C, D
Fragment: Residues 299-347 And 360-714
Synonym: Dpde3, Pde43
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde4d, Dpde3
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.129 75.311 162.559 90.00 92.43 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA, D71, MG, ZN enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceDesign of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety., Burgin AB, Magnusson OT, Singh J, Witte P, Staker BL, Bjornsson JM, Thorsteinsdottir M, Hrafnsdottir S, Hagen T, Kiselyov AS, Stewart LJ, Gurney ME, Nat Biotechnol. 2009 Dec 27. PMID:20037581
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk]
  • Biological Unit Coordinates (3g4g.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (3g4g.pdb2.gz) 58 Kb
  • Biological Unit Coordinates (3g4g.pdb3.gz) 59 Kb
  • Biological Unit Coordinates (3g4g.pdb4.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 3G4G
  • CSU: Contacts of Structural Units for 3G4G
  • Structure Factors (1018 Kb)
  • Retrieve 3G4G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G4G from S2C, [Save to disk]
  • Re-refined 3g4g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G4G 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 3G4G
  • 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 3G4G, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g4g_D] [3g4g_A] [3g4g_C] [3g4g_B] [3g4g]
  • SWISS-PROT database: [Q08499]
  • Domain organization of [PDE4D_HUMAN] by SWISSPFAM
  • Domain found in 3G4G: [HDc ] by SMART
  • Other resources with information on 3G4G
  • Community annotation for 3G4G 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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