4WOR

Staphylococcal nuclease in complex with Ca2+ and thymidine-3'-5'-diphosphate (pdTp) at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 4WOR

Classification: HYDROLASE / HYDROLASE inhibitor

Total Structure Weight: 17285.60

Macromolecule Entities
Molecule Chains Length Organism Details
Thermonuclease A 149 Staphylococcus aureus EC#: 3.1.31.1 IUBMB
Gene Name(s): nuc
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A THYMIDINE-3',5'-DIPHOSPHATE
C10 H16 N2 O11 P2
CSNCBOPUCJOHLS-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.180
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 48.50 α = 90.00
b = 48.50 β = 90.00
c = 63.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-10-16
  • Released Date: 2014-10-29
  • Deposition author(s): Wall, M.E., Ealick, S.E., Gruner, S.M.

Revision History

  • Version 1_0: 2014-10-29

    Type: Initial release

  • Version 2_0: 2017-09-20

    Type: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy