5DFH Lyase Dna date Aug 26, 2015
title Human Ape1 Mismatch Product Complex
authors B.D.Freudenthal, S.H.Wilson
compound source
Molecule: Dna-(Apurinic Or Apyrimidinic Site) Lyase
Chain: A, B
Synonym: Apex Nuclease,Apen,Apurinic-Apyrimidinic Endonucle 1,Ref-1,Redox Factor-1;
Ec: 3.1.-.-,4.2.99.18
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apex1, Ape, Ape1, Apex, Apx, Hap1, Ref1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_cell_line: Bl21-De3

Molecule: Dna (5'-D(P(3dr)Pcpgpapcpgpgpaptpcpc)-
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpgpgpcpgpcpaptpcpap 3');
Chain: V
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpt)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.179 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.434 61.603 72.277 83.86 78.76 88.19
method X-Ray Diffractionresolution 1.95 Å
ligand 3DR, EDO, MG enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCapturing snapshots of APE1 processing DNA damage., Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH, Nat Struct Mol Biol. 2015 Nov;22(11):924-31. doi: 10.1038/nsmb.3105. Epub 2015, Oct 12. PMID:26458045
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (5dfh.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (5dfh.pdb2.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 5DFH
  • CSU: Contacts of Structural Units for 5DFH
  • Structure Factors (526 Kb)
  • Retrieve 5DFH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DFH from S2C, [Save to disk]
  • Re-refined 5dfh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DFH 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 5DFH
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dfh_D] [5dfh_B] [5dfh_C] [5dfh_V] [5dfh_A] [5dfh]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5DFH
  • Community annotation for 5DFH at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science