6BOR Dna Binding Protein Dna date Nov 20, 2017
title Human Ape1 Substrate Complex With An Gg Mismatch Adjacent T
authors B.D.Freudenthal, A.M.Whitaker, M.S.Fairlamb
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: 21-Mer Dna
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 21-Mer Dna
Chain: V
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.170 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.408 60.204 73.014 82.94 80.29 89.10
method X-Ray Diffractionresolution 1.84 Å
ligand 3DR, CL, EDO enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • transcription corepressor ac...
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity
  • RNA-DNA hybrid ribonuclease ...
  • exonuclease activity
  • phosphodiesterase I activity...
  • double-stranded DNA 3'-5' ex...
  • 3'-5' exonuclease activity
  • oxidoreductase activity


  • Primary referenceApurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches., Fairlamb MS, Whitaker AM, Freudenthal BD, Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):760-768. doi:, 10.1107/S2059798318003340. Epub 2018 Jul 24. PMID:30082511
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (6bor.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (6bor.pdb2.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 6BOR
  • CSU: Contacts of Structural Units for 6BOR
  • Structure Factors (775 Kb)
  • Retrieve 6BOR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6BOR from S2C, [Save to disk]
  • View 6BOR 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 6BOR
  • 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 6bor from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6bor_V] [6bor_B] [6bor_P] [6bor_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6BOR
  • Community annotation for 6BOR at PDBWiki (http://pdbwiki.org)

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