5WN3	Hydrolase, Lyase Dna	date	Jul 31, 2017
title	Ape1 F266a Exonuclease Substrate Complex With A Ct Mismatch
authors	B.D.Freudenthal, A.M.Whitaker
compound		source
Molecule: Dna (5'-D(Ptpcpgpapcpgpgpaptpcpc)-3') Chain: C Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(Dv3))-3') Chain: D Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpaptpcpgpcpaptpcpap 3'); Chain: E Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna-(Apurinic Or Apyrimidinic Site) Lyase Chain: A, B Synonym: Apex1, Apex Nuclease,Apen,Apurinic-Apyrimidinic En 1, Ape-1, Ref-1, Redox Factor-1; Ec: 3.1.-.-, 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 Bl21 (De3) Expression_system_taxid: 469008
symmetry	Space Group: P 1 21 1	R_factor 0.210 R_Free 0.258
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.144 65.545 91.441 90.00 110.08 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	C7R, CA, CL, EDO, NA	enzyme	Hydrolase E.C.3.1 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Molecular snapshots of APE1 proofreading mismatches and removing DNA damage., Whitaker AM, Flynn TS, Freudenthal BD, Nat Commun. 2018 Jan 26;9(1):399. doi: 10.1038/s41467-017-02175-y. PMID:29374164

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk] Biological Unit Coordinates (5wn3.pdb1.gz) 67 Kb Biological Unit Coordinates (5wn3.pdb2.gz) 48 Kb LPC: Ligand-Protein Contacts for 5WN3 CSU: Contacts of Structural Units for 5WN3 Structure Factors (417 Kb) Retrieve 5WN3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5WN3 from S2C, [Save to disk]

View 5WN3 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 5WN3

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5wn3_C] [5wn3_A] [5wn3_B] [5wn3_E] [5wn3_D] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5WN3

Community annotation for 5WN3 at PDBWiki (http://pdbwiki.org)

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