5DFJ	Lyase Dna	date	Aug 26, 2015
title	Human Ape1 E96qd210n Mismatch Substrate 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: 4.2.99.18 Engineered: Yes Mutation: 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: 469008 Expression_system_cell_line: Bl21-De3
Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgptp(3dr) Pcpgpapcpgpgpaptpcpc)-3'); Chain: P 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
symmetry	Space Group: P 1	R_factor 0.159 R_Free 0.200
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.462 60.668 73.161 82.78 80.28 89.20
method	X-Ray Diffraction	resolution	1.85 Å
ligand	3DR, CL, EDO	enzyme	Lyase E.C.4.2.99.18 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Capturing 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] (123 Kb) [Save to disk] Biological Unit Coordinates (5dfj.pdb1.gz) 72 Kb Biological Unit Coordinates (5dfj.pdb2.gz) 48 Kb LPC: Ligand-Protein Contacts for 5DFJ CSU: Contacts of Structural Units for 5DFJ Structure Factors (610 Kb) Retrieve 5DFJ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5DFJ from S2C, [Save to disk] Re-refined 5dfj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DFJ 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 5DFJ

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: [5dfj_V] [5dfj_B] [5dfj_A] [5dfj_P] [5dfj] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5DFJ

Community annotation for 5DFJ at PDBWiki (http://pdbwiki.org)

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