5WN0 Hydrolase, Lyase Dna date Jul 31, 2017
title Ape1 Exonuclease Substrate Complex With A Cg Match
authors B.D.Freudenthal, A.M.Whitaker
compound source
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
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

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpapgpcpgpcpaptpcpap 3');
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.217 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.264 61.942 73.765 82.59 76.88 85.89
method X-Ray Diffractionresolution 2.60 Å
ligand
enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMolecular 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] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (5wn0.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (5wn0.pdb2.gz) 45 Kb
  • CSU: Contacts of Structural Units for 5WN0
  • Structure Factors (303 Kb)
  • Retrieve 5WN0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5WN0 from S2C, [Save to disk]
  • View 5WN0 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 5WN0
  • 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
  • Fold representative 5wn0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5wn0_A] [5wn0_B] [5wn0_C] [5wn0_E] [5wn0_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5WN0
  • Community annotation for 5WN0 at PDBWiki (http://pdbwiki.org)

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