3DYS Hydrolase date Jul 28, 2008
title Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaki 20mm Cgmp+20 Mm Mncl2+20 Mm Mgcl2 For 2 Hours, And Flash-Co Liquid Nitrogen Temperature When Substrate Was Still Abudan
authors S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti
compound source
Molecule: High Affinity Cgmp-Specific 3',5'-Cyclic Phosphod 9a;
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 0.186 R_Free 0.212
length a length b length c angle alpha angle beta angle gamma
103.992 103.992 269.762 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 5GP, FMT, IBM, MG, MN BindingDB enzyme Hydrolase E.C. BRENDA
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] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (3dys.pdb1.gz) 118 Kb
  • Biological Unit Coordinates (3dys.pdb2.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 3DYS
  • CSU: Contacts of Structural Units for 3DYS
  • Likely Quarternary Molecular Structure file(s) for 3DYS
  • Structure Factors (527 Kb)
  • Retrieve 3DYS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DYS from S2C, [Save to disk]
  • Re-refined 3dys structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DYS 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 3DYS
  • 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 3DYS, from MSDmotif at EBI
  • Fold representative 3dys from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dys_B] [3dys] [3dys_A]
  • SWISS-PROT database: [O76083]
  • Domain organization of [PDE9A_HUMAN] by SWISSPFAM
  • Domain found in 3DYS: [HDc ] by SMART
  • Other resources with information on 3DYS
  • Community annotation for 3DYS 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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