2YY2 Hydrolase date Apr 27, 2007
title Crystal Structure Of The Human Phosphodiesterase 9a Catalytic Domain Complexed With Ibmx
authors N.Handa, M.Shirouzu, T.Terada, K.Omori, J.Kotera, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: High-Affinity Cgmp-Specific 3',5'-Cyclic Phosphodiesterase 9a;
Chain: A, B
Fragment: Catalytic Domain, Unp Residues 241-566
Ec: 3.1.4.35
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Px050225-12
Other_details: E. Coli Cell Free System
symmetry Space Group: P 41 21 2
R_factor 0.206 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.270 104.270 269.610 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand IBM, MG, ZN BindingDB enzyme Hydrolase E.C.3.1.4.35 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (2yy2.pdb1.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 2YY2
  • CSU: Contacts of Structural Units for 2YY2
  • Likely Quarternary Molecular Structure file(s) for 2YY2
  • Structure Factors (627 Kb)
  • Retrieve 2YY2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YY2 from S2C, [Save to disk]
  • Re-refined 2yy2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YY2 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 2YY2
  • 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 2YY2, from MSDmotif at EBI
  • Fold representative 2yy2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yy2] [2yy2_B] [2yy2_A]
  • SWISS-PROT database: [O76083]
  • Domain organization of [PDE9A_HUMAN] by SWISSPFAM
  • Domain found in 2YY2: [HDc ] by SMART
  • Other resources with information on 2YY2
  • Community annotation for 2YY2 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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