6W2P Dna Binding Protein Dna date Mar 06, 2020
title Ape1 Endonuclease Product Complex L104r
authors B.D.Freudenthal, A.M.Whitaker
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
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

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

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

Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpaptpcpgpcpaptpcpap 3');
Chain: V
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.201 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.387 61.780 72.278 83.71 78.56 88.02
method X-Ray Diffractionresolution 1.94 Å
ligand 3DR, EDO, MG 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] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (6w2p.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (6w2p.pdb2.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 6W2P
  • CSU: Contacts of Structural Units for 6W2P
  • Structure Factors (1312 Kb)
  • Retrieve 6W2P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6W2P from S2C, [Save to disk]
    • View 6W2P 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 6W2P
  • 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: [6w2p_D] [6w2p_P] [6w2p_A] [6w2p_B] [6w2p_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6W2P
  • Community annotation for 6W2P at PDBWiki (http://pdbwiki.org)

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