3ECM Hydrolase date Sep 01, 2008
title Crystal Structure Of The Unliganded Pde8a Catalytic Domain
authors H.Wang, Z.Yan, S.Yang, J.Cai, H.Robinson, H.Ke
compound source
Molecule: High Affinity Camp-Specific And Ibmx-Insensitive 3',5'-Cyclic Phosphodiesterase 8a;
Chain: A
Fragment: The Catalytic Domain Of Pde8a1 (Unp Residues 482- 819);
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde8a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: C 2 2 21
R_factor 0.236 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.261 132.661 101.517 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand MG, ZN enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceKinetic and Structural Studies of Phosphodiesterase-8A and Implication on the Inhibitor Selectivity., Wang H, Yan Z, Yang S, Cai J, Robinson H, Ke H, Biochemistry. 2008 Nov 5. PMID:18983167
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (3ecm.pdb1.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 3ECM
  • CSU: Contacts of Structural Units for 3ECM
  • Likely Quarternary Molecular Structure file(s) for 3ECM
  • Structure Factors (431 Kb)
  • Retrieve 3ECM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ECM from S2C, [Save to disk]
  • Re-refined 3ecm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ECM 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 3ECM
  • 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 3ECM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ecm] [3ecm_A]
  • SWISS-PROT database: [O60658]
  • Domain organization of [PDE8A_HUMAN] by SWISSPFAM
  • Domain found in 3ECM: [HDc ] by SMART
  • Other resources with information on 3ECM
  • Community annotation for 3ECM 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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