3DYL Hydrolase date Jul 28, 2008
title Human Phosphdiesterase 9 Substrate Complex (Es Complex)
authors S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti
compound source
Molecule: Human Phosphodiesterase 9
Chain: A, B
Fragment: Catalytic Domain, Unp Residues 242-566
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde9a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.188 R_Free 0.219
length a length b length c angle alpha angle beta angle gamma
103.787 103.787 269.799 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand FMT, IBM, MG, MN, PCG BindingDB enzyme Hydrolase E.C. BRENDA
A, B

Primary referenceStructural basis for the catalytic mechanism of human phosphodiesterase 9., Liu S, Mansour MN, Dillman KS, Perez JR, Danley DE, Aeed PA, Simons SP, Lemotte PK, Menniti FS, Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13309-14. Epub 2008 Aug 29. PMID:18757755
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk]
  • Biological Unit Coordinates (3dyl.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (3dyl.pdb2.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 3DYL
  • CSU: Contacts of Structural Units for 3DYL
  • Likely Quarternary Molecular Structure file(s) for 3DYL
  • Structure Factors (428 Kb)
  • Retrieve 3DYL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DYL from S2C, [Save to disk]
  • Re-refined 3dyl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DYL 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 3DYL
  • 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 3DYL, from MSDmotif at EBI
  • Fold representative 3dyl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dyl_B] [3dyl_A] [3dyl]
  • SWISS-PROT database: [O76083]
  • Domain organization of [PDE9A_HUMAN] by SWISSPFAM
  • Domain found in 3DYL: [HDc ] by SMART
  • Other resources with information on 3DYL
  • Community annotation for 3DYL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science