2FM0 Hydrolase date Jan 06, 2006
title Crystal Structure Of Pde4d In Complex With L-869298
authors Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huan
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d
Chain: A, B, C, D
Fragment: Catalytic Domain
Synonym: Dpde3, Pde43
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde4d2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (Codonplus)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.511 112.176 160.174 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand M98, MG, ZN BindingDB enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceEnantiomer Discrimination Illustrated by the High Resolution Crystal Structures of Type 4 Phosphodiesterase., Huai Q, Sun Y, Wang H, Macdonald D, Aspiotis R, Robinson H, Huang Z, Ke H, J Med Chem. 2006 Mar 23;49(6):1867-1873. PMID:16539372
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (226 Kb) [Save to disk]
  • Biological Unit Coordinates (2fm0.pdb1.gz) 219 Kb
  • LPC: Ligand-Protein Contacts for 2FM0
  • CSU: Contacts of Structural Units for 2FM0
  • Likely Quarternary Molecular Structure file(s) for 2FM0
  • Structure Factors (1690 Kb)
  • Retrieve 2FM0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FM0 from S2C, [Save to disk]
  • Re-refined 2fm0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FM0 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 2FM0
  • 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 2FM0, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fm0_B] [2fm0] [2fm0_C] [2fm0_A] [2fm0_D]
  • SWISS-PROT database: [Q08499]
  • Domain organization of [PDE4D_HUMAN] by SWISSPFAM
  • Domain found in 2FM0: [HDc ] by SMART
  • Other resources with information on 2FM0
  • Community annotation for 2FM0 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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