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PDBsum entry 2wey

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2wey
Jmol
Contents
Protein chain
324 a.a. *
Ligands
EV1 ×2
Metals
_MG ×2
_ZN ×2
Waters ×23
* Residue conservation analysis
PDB id:
2wey
Name: Hydrolase
Title: Human pde-papaverine complex obtained by ligand soaking of cross-linked protein crystals
Structure: Camp and camp-inhibited cgmp 3', 5'-cyclic phosphodiesterase. Chain: a, b. Fragment: catalytic domain, residues 467-807. Synonym: phosphodiesterase 10a2, pde10a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.242     R-free:   0.300
Authors: O.A.Andersen,D.L.Schonfeld,I.Toogood-Johnson,B.Felicetti, C.Albrecht,T.Fryatt,M.Whittaker,D.Hallett,J.Barker
Key ref:
O.A.Andersen et al. (2009). Cross-linking of protein crystals as an aid in the generation of binary protein-ligand crystal complexes, exemplified by the human PDE10a-papaverine structure. Acta Crystallogr D Biol Crystallogr, 65, 872-874. PubMed id: 19622871 DOI: 10.1107/S0907444909017855
Date:
02-Apr-09     Release date:   28-Jul-09    
PROCHECK
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 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 324 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.3.1.4.17  - 3',5'-cyclic-nucleotide phosphodiesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate
Nucleoside 3',5'-cyclic phosphate
+ H(2)O
= nucleoside 5'-phosphate
   Enzyme class 2: E.C.3.1.4.35  - 3',5'-cyclic-GMP phosphodiesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate
Guanosine 3',5'-cyclic phosphate
+ H(2)O
= guanosine 5'-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444909017855 Acta Crystallogr D Biol Crystallogr 65:872-874 (2009)
PubMed id: 19622871  
 
 
Cross-linking of protein crystals as an aid in the generation of binary protein-ligand crystal complexes, exemplified by the human PDE10a-papaverine structure.
O.A.Andersen, D.L.Schönfeld, I.Toogood-Johnson, B.Felicetti, C.Albrecht, T.Fryatt, M.Whittaker, D.Hallett, J.Barker.
 
  ABSTRACT  
 
Protein crystallography has proven to be an effective method of obtaining high-resolution structures of protein-ligand complexes. However, in certain cases only apoprotein structures are readily available and the generation of crystal complexes is more problematic. Some crystallographic systems are not amenable to soaking of ligands owing to crystal-packing effects and many protein-ligand complexes do not crystallize under the same conditions as used for the apoprotein. Using crystals of human phosphodiesterase 10a (hPDE10a) as an example of such a challenging crystallographic system, the structure of the complex with papaverine was obtained to 2.8 A resolution using protein crystals cross-linked by glutaraldehyde prior to soaking of the ligand. Inspection of the electron-density maps suggested that the correct mode of binding was obtained in one of the two monomers in the asymmetric unit and inspection of crystal-packing contacts explained why cocrystallization experiments and soaking of crystals that were not cross-linked were unsuccessful.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Stereo figure of the active site of monomer B in the hPDE10a-papaverine crystal structure. F[o] - F[c] electron density is contoured at 2.0 . Hydrogen-bonding interactions are shown as dotted lines to Gln726. The protein and papaverine are shown as a stick models with green and magenta C atoms, respectively. Zinc and magnesium are shown as purple and red spheres, respectively.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 872-874) copyright 2009.  
  Figure was selected by an automated process.