3VSY

High-resolution crystal structure of wild-type KSI in the apo form at neutral pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Incorporation of rapid thermodynamic data in fragment-based drug discovery.

Kobe, A.Caaveiro, J.M.M.Tashiro, S.Kajihara, D.Kikkawa, M.Mitani, T.Tsumoto, K.

(2013) J.Med.Chem. 56: 2155-2159

  • DOI: 10.1021/jm301603n

  • PubMed Abstract: 
  • Fragment-based drug discovery (FBDD) has enjoyed increasing popularity in recent years. We introduce SITE (single-injection thermal extinction), a novel thermodynamic methodology that selects high-quality hits early in FBDD. SITE is a fast calorimetr ...

    Fragment-based drug discovery (FBDD) has enjoyed increasing popularity in recent years. We introduce SITE (single-injection thermal extinction), a novel thermodynamic methodology that selects high-quality hits early in FBDD. SITE is a fast calorimetric competitive assay suitable for automation that captures the essence of isothermal titration calorimetry but using significantly fewer resources. We describe the principles of SITE and identify a novel family of fragment inhibitors of the enzyme ketosteroid isomerase displaying high values of enthalpic efficiency.


    Organizational Affiliation

    Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Steroid Delta-isomerase
A, B
132Pseudomonas putidaGene Names: ksi
EC: 5.3.3.1
Find proteins for P07445 (Pseudomonas putida)
Go to UniProtKB:  P07445
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.563α = 90.00
b = 73.353β = 90.00
c = 95.549γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
SERGUIdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description