2ZMF Hydrolase date Apr 17, 2008
title Crystal Structure Of The C-Terminal Gaf Domain Of Human Phosphodiesterase 10a
authors N.Handa, S.Kishishita, E.Mizohata, K.Omori, J.Kotera, T.Terada, M. S.Yokoyama, Riken Structural Genomicsproteomics Initiative
compound source
Molecule: Camp And Camp-Inhibited Cgmp 3',5'-Cyclic Phospho 10a;
Chain: A, B
Fragment: C-Terminal Gaf Domain
Ec: 3.1.4.17
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde10a
Expression_system: Cell Free (Escherichia Coli)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Px060608-01
symmetry Space Group: P 31 2 1
R_factor 0.199 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.506 74.506 146.524 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand CMP, MSE enzyme Hydrolase E.C.3.1.4.17 BRENDA
note 2ZMF supersedes 2E4S
Primary referenceCrystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP., Handa N, Mizohata E, Kishishita S, Toyama M, Morita S, Uchikubo-Kamo T, Akasaka R, Omori K, Kotera J, Terada T, Shirouzu M, Yokoyama S, J Biol Chem. 2008 Jul 11;283(28):19657-64. Epub 2008 May 13. PMID:18477562
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (2zmf.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 2ZMF
  • CSU: Contacts of Structural Units for 2ZMF
  • Likely Quarternary Molecular Structure file(s) for 2ZMF
  • Structure Factors (987 Kb)
  • Retrieve 2ZMF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZMF from S2C, [Save to disk]
  • Re-refined 2zmf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2ZMF 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 2ZMF
  • 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 2ZMF, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zmf_B] [2zmf] [2zmf_A]
  • SWISS-PROT database: [Q9Y233]
  • Domain organization of [PDE10_HUMAN] by SWISSPFAM
  • Domain found in 2ZMF: [GAF ] by SMART
    • Other resources with information on 2ZMF
  • Community annotation for 2ZMF 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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