3GH3 Hydrolase date Mar 02, 2009
title Structural Insights Into The Catalytic Mechanism Of Cd38: Ev A Conformationally Flexible Covalent Enzyme-Substrate Compl
authors P.F.Egea, H.Muller-Steffner, R.M.Stroud, E.Kellenberger, N.Oppen F.Schuber
compound source
Molecule: Ecto-Nad+ Glycohydrolase (Cd38 Molecule)
Chain: A, B
Fragment: Unp Residues 32-278
Ec: 3.2.2.5
Engineered: Yes
Organism_scientific: Bos Taurus
Organism_common: Bovine,Cow,Domestic Cattle,Domestic Cow
Organism_taxid: 9913
Gene: Cd38, Cd38 Gene From Bos Taurus
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.483 80.879 151.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CAC, NAG, SO4 enzyme Hydrolase E.C.3.2.2.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceInsights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its michaelis complex and covalently-trapped intermediates., Egea PF, Muller-Steffner H, Kuhn I, Cakir-Kiefer C, Oppenheimer NJ, Stroud RM, Kellenberger E, Schuber F, PLoS One. 2012;7(4):e34918. Epub 2012 Apr 18. PMID:22529956
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (3gh3.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (3gh3.pdb2.gz) 47 Kb
  • Biological Unit Coordinates (3gh3.pdb3.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 3GH3
  • CSU: Contacts of Structural Units for 3GH3
  • Structure Factors (382 Kb)
  • Retrieve 3GH3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GH3 from S2C, [Save to disk]
  • Re-refined 3gh3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GH3 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 3GH3
  • 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 3GH3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gh3_B] [3gh3] [3gh3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3GH3
  • Community annotation for 3GH3 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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