5DG0 Hydrolase,Lyase Dna date Aug 27, 2015
title Human Ape1 Phosphorothioate Substrate Complex With Mn2+
authors B.D.Freudenthal, S.H.Wilson
compound source
Molecule: Dna-(Apurinic Or Apyrimidinic Site) Lyase
Chain: A, B
Fragment: Unp Residues 43-318
Synonym: Apex Nuclease,Apen,Apurinic-Apyrimidinic Endonucle 1,Ref-1,Redox Factor-1;
Ec: 3.1.-.-,
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apex1, Ape, Ape1, Apex, Apx, Hap1, Ref1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(Omc)P(48z Pcpgpapcpgpgpaptpcpc)-3');
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpgpgpcpgpcpaptpcpap 3');
Chain: V
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.166 R_Free 0.205
length a length b length c angle alpha angle beta angle gamma
44.365 60.601 73.316 83.12 80.68 89.04
method X-Ray Diffractionresolution 1.80 Å
ligand 48Z, CL, EDO, MN, OMC enzyme Hydrolase E.C.3.1 BRENDA
A, B

Primary referenceCapturing snapshots of APE1 processing DNA damage., Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH, Nat Struct Mol Biol. 2015 Nov;22(11):924-31. doi: 10.1038/nsmb.3105. Epub 2015, Oct 12. PMID:26458045
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (5dg0.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (5dg0.pdb2.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 5DG0
  • CSU: Contacts of Structural Units for 5DG0
  • Structure Factors (996 Kb)
  • Retrieve 5DG0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DG0 from S2C, [Save to disk]
  • Re-refined 5dg0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DG0 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 5DG0
  • 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 5dg0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dg0_A] [5dg0_V] [5dg0_B] [5dg0_P] [5dg0]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DG0
  • Community annotation for 5DG0 at PDBWiki (http://pdbwiki.org)

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