5V08

Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA (rVI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 5V08

Classification: HYDROLASE / DNA

Total Structure Weight: 46608.40


Macromolecule Entities
Molecule Chains Length Organism Details
Exonuclease 1 Z 352 Homo sapiens EC#: 3.1 IUBMB
Fragment: UNP residues 1-352
Mutation: D173A
Gene Name(s): EXO1 Gene View EXOI HEX1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3') A 13 Synthetic construct
DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3') B 10 Synthetic construct

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

B, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

Z SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.215
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 74.26 α = 90.00
b = 74.26 β = 90.00
c = 179.38 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-28
  • Released Date: 2017-05-24
  • Deposition author(s): Shi, Y., Beese, L.S.

Revision History

  • 2017-06-07
    Type: Database references
  • 2017-06-21
    Type: Database references
  • 2017-09-13
    Type: Author supporting evidence