3F6Y Hydrolase date Nov 07, 2008
title Conformational Closure Of The Catalytic Site Of Human Cd38 I Calcium
authors Q.Liu, R.Graeff, I.A.Kriksunov, C.M.C.Lam, H.C.Lee, Q.Hao
compound source
Molecule: Adp-Ribosyl Cyclase 1
Chain: A
Fragment: Enzymatic Domain, Extracellular Domain
Synonym: Cyclic Adp-Ribose Hydrolase 1, Cadpr Hydrolase 1, Antigen;
Ec: 3.2.2.5
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd38
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: X-33
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppiczalphaa
symmetry Space Group: C 1 2 1
R_factor 0.146 R_Free 0.184
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.687 60.058 56.932 90.00 129.69 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand CA enzyme Hydrolase E.C.3.2.2.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceConformational Closure of the Catalytic Site of Human CD38 Induced by Calcium., Liu Q, Graeff R, Kriksunov IA, Lam CM, Lee HC, Hao Q, Biochemistry. 2008 Dec 30;47(52):13966-73. PMID:19117080
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (3f6y.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (3f6y.pdb2.gz) 171 Kb
  • LPC: Ligand-Protein Contacts for 3F6Y
  • CSU: Contacts of Structural Units for 3F6Y
  • Likely Quarternary Molecular Structure file(s) for 3F6Y
  • Structure Factors (274 Kb)
  • Retrieve 3F6Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F6Y from S2C, [Save to disk]
  • Re-refined 3f6y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F6Y 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 3F6Y
  • 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 3F6Y, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f6y_A] [3f6y]
  • SWISS-PROT database: [P28907]
  • Domain organization of [CD38_HUMAN] by SWISSPFAM
  • Other resources with information on 3F6Y
  • Community annotation for 3F6Y 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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