3SL3 Hydrolase date Jun 24, 2011
title Crystal Structure Of The Apo Form Of The Catalytic Domain Of
authors S.F.Feil
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d
Chain: A, B, C, D
Fragment: Catalytic Domain, Unp Residues 381-741
Synonym: Dpde3, Pde43
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpde3, Pde4d
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Star Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.269 111.757 160.279 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand DMS, EDO, EPE, PEG, PO4, ZN enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceThiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2., Nankervis JL, Feil SC, Hancock NC, Zheng Z, Ng HL, Morton CJ, Holien JK, Ho PW, Frazzetto MM, Jennings IG, Manallack DT, Martin TJ, Thompson PE, Parker MW, Bioorg Med Chem Lett. 2011 Dec 1;21(23):7089-93. Epub 2011 Oct 5. PMID:22030030
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (234 Kb) [Save to disk]
  • Biological Unit Coordinates (3sl3.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (3sl3.pdb2.gz) 59 Kb
  • Biological Unit Coordinates (3sl3.pdb3.gz) 60 Kb
  • Biological Unit Coordinates (3sl3.pdb4.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3SL3
  • CSU: Contacts of Structural Units for 3SL3
  • Structure Factors (1207 Kb)
  • Retrieve 3SL3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SL3 from S2C, [Save to disk]
  • Re-refined 3sl3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SL3 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 3SL3
  • 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 3SL3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sl3_C] [3sl3_D] [3sl3] [3sl3_A] [3sl3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SL3: [HDc ] by SMART
  • Other resources with information on 3SL3
  • Community annotation for 3SL3 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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