4PDS

Crystal structure of Rad53 kinase domain and SCD2 in complex with AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.227

Literature

Macromolecules
Sequence Display for 4PDS

Classification: TRANSFERASE

Total Structure Weight: 77865.72

Macromolecule Entities
Molecule Chains Length Organism Details
Serine/threonine-protein kinase RAD53 A, B 347 Saccharomyces cerevisiae EC#: 2.7.12.1 IUBMB
Fragment: Kinase domain and SCD2 (UNP residues 170-512)
Mutation: A225S, D339A
Gene Name(s): RAD53 MEC2 SAD1 SPK1 YPL153C P2588
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ANP
Query on ANP

A, B PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.227
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 74.15 α = 90.00
b = 77.54 β = 90.00
c = 222.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-04-21
  • Released Date: 2014-05-28
  • Deposition author(s): Ho, C.S., Wybenga-Groot, L.E., Ceccarelli, D.F., Sicheri, F.

Revision History

  • Version 1_0: 2014-05-28

    Type: Initial release

  • Version 1_1: 2014-10-01

    Type: Database references

  • Version 1_2: 2017-11-22

    Type: Derived calculations, Other, Refinement description, Source and taxonomy