6W3U Dna Binding Protein Dna date Mar 09, 2020
title Ape1 Exonuclease Substrate Complex R237c
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(C7r))-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: Apex Nuclease,Apen,Apurinic-Apyrimidinic Endonucle 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
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.184 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.177 65.622 91.717 90.00 110.52 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand C7R, C7S, CA, CL, EDO, NA enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMolecular and structural characterization of disease-associated APE1 polymorphisms., Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD, DNA Repair (Amst). 2020 May 16;91-92:102867. doi: 10.1016/j.dnarep.2020.102867. PMID:32454397
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (6w3u.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (6w3u.pdb2.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 6W3U
  • CSU: Contacts of Structural Units for 6W3U
  • Structure Factors (834 Kb)
  • Retrieve 6W3U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6W3U from S2C, [Save to disk]
  • View 6W3U 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 6W3U
  • 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 6w3u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6w3u_A] [6w3u_E] [6w3u_D] [6w3u_B] [6w3u_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6W3U
  • Community annotation for 6W3U at PDBWiki (http://pdbwiki.org)

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