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.-.-,4.2.99.18 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
crystal cell	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 Diffraction	resolution	1.80 Å
ligand	48Z, CL, EDO, MN, OMC	enzyme	Hydrolase E.C.3.1 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Capturing 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] (121 Kb) [Save to disk] Biological Unit Coordinates (5dg0.pdb1.gz) 70 Kb Biological Unit Coordinates (5dg0.pdb2.gz) 47 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

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: [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)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---