2O3H Lyase date Dec 01, 2006
title Crystal Structure Of The Human C65a Ape
authors M.M.Georgiadis, R.K.Gaur, S.Delaplane, J.Svenson
compound source
Molecule: Dna-(Apurinic Or Apyrimidinic Site) Lyase
Chain: A
Synonym: Ap Endonuclease 1, Apex Nuclease, Apen, Ref-1 Prot Apurinicapyrimidinic Endonuclease;
Ec: 4.2.99.18
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apex1, Ape, Apex, Apx, Hap1, Ref1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 21 21 2
R_factor 0.177 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.693 143.604 45.385 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACT, SM enzyme Lyase E.C.4.2.99.18 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceEvolution of the redox function in mammalian apurinic/apyrimidinic endonuclease., Georgiadis MM, Luo M, Gaur RK, Delaplane S, Li X, Kelley MR, Mutat Res. 2008 Aug 25;643(1-2):54-63. Epub 2008 May 18. PMID:18579163
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (2o3h.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 2O3H
  • CSU: Contacts of Structural Units for 2O3H
  • Likely Quarternary Molecular Structure file(s) for 2O3H
  • Structure Factors (451 Kb)
  • Retrieve 2O3H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O3H from S2C, [Save to disk]
  • Re-refined 2o3h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2O3H 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 2O3H
  • 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 2O3H, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o3h_A] [2o3h]
  • SWISS-PROT database: [P27695]
  • Domain organization of [APEX1_HUMAN] by SWISSPFAM
  • Other resources with information on 2O3H
  • Community annotation for 2O3H 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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