2VOA Lyase date Feb 11, 2008
title Structure Of An Ap Endonuclease From Archaeoglobus Fulgidus
authors E.B.Kuettner, R.Schmiedel, T.Greiner-Stoffele, N.Strater
compound source
Molecule: Exodeoxyribonuclease III
Chain: A, B
Synonym: Af_exo, Xtha
Engineered: Yes
Mutation: Yes
Organism_scientific: Archaeoglobus Fulgidus
Organism_taxid: 2234
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami B(De3)-Ril
Expression_system_plasmid: Pet28
Other_details: Dsm4304

Molecule: 5'-D(Gpcpgpgptpapgpcpcpgp)-3'
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Cpgpgpcptpapcpcpgpcp)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.198 R_Free 0.230
length a length b length c angle alpha angle beta angle gamma
67.786 60.817 72.349 90.00 91.22 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand OCS enzyme Lyase E.C. BRENDA
A, B
  • nuclease activity
  • endonuclease activity

  • Primary referenceStructure and function of the abasic site specificity pocket of an AP endonuclease from Archaeoglobus fulgidus., Schmiedel R, Kuettner EB, Keim A, Strater N, Greiner-Stoffele T, DNA Repair (Amst). 2008 Dec 4. PMID:19015049
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (2voa.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 2VOA
  • CSU: Contacts of Structural Units for 2VOA
  • Likely Quarternary Molecular Structure file(s) for 2VOA
  • Structure Factors (453 Kb)
  • Retrieve 2VOA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VOA from S2C, [Save to disk]
  • Re-refined 2voa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VOA 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 2VOA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VOA, from MSDmotif at EBI
  • Fold representative 2voa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2voa_D] [2voa_C] [2voa_A] [2voa_B] [2voa]
  • SWISS-PROT database: [O29675]
  • Domain organization of [O29675_ARCFU] by SWISSPFAM
  • Other resources with information on 2VOA
  • Community annotation for 2VOA 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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