6W4T Lyase Dna date Mar 11, 2020
title Ape1 Y269a Phosphorothioate Substrate Complex With Abasic Dn
authors B.D.Freudenthal, N.M.Hoitsma
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(Pgpcptpgpaptpgpcpgptp(48z) Pcpgpapcpgpgpaptpcpc)-3');
Chain: P, C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpgpapcpgpcpaptpcpap 3');
Chain: V, F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.659 148.315 153.235 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.77 Å
ligand DV3 enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (6w4t.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (6w4t.pdb2.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 6W4T
  • CSU: Contacts of Structural Units for 6W4T
  • Structure Factors (773 Kb)
  • Retrieve 6W4T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6W4T from S2C, [Save to disk]
    • View 6W4T 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 6W4T
  • 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: [6w4t_P] [6w4t_A] [6w4t_V] [6w4t_F] [6w4t_C] [6w4t_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6W4T
  • Community annotation for 6W4T at PDBWiki (http://pdbwiki.org)

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