4ABD

Fragments bound to bovine trypsin for the SAMPL challenge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Dingo Dataset: A Comprehensive Set of Data for the Sampl Challenge.

Newman, J.Dolezal, O.Fazio, V.Caradoc-Davies, T.Peat, T.S.

(2012) J.Comput.Aided Mol.Des. 26: 497

  • DOI: 10.1007/s10822-011-9521-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using ...

    Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies.


    Related Citations: 
    • Fragment Screening for the Modelling Community: Spr, Itc, and Crystallography
      Dolezal, O.,Doughty, L.,Hattarki, M.K.,Fazio, V.J.,Caradoc-Davies, T.T.,Newman, J.,Peat, T.S.
      (2013) Aust.J.Chem. 66: 1507
    • Practical Aspects of the Sampl Challenge: Providing an Extensive Experimental Data Set for the Modeling Community.
      Newman, J.,Fazio, V.J.,Caradoc-Davies, T.T.,Branson, K.,Peat, T.S.
      (2009) J.Biomol.Screen 14: 1245


    Organizational Affiliation

    CSIRO Division of Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATIONIC TRYPSIN
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SW2
Query on SW2

Download SDF File 
Download CCD File 
A
1-[3-(1H-pyrrol-1-yl)phenyl]methanamine
C11 H12 N2
XLBYUDUEHVKUKQ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
ethane-1,2-diol
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SW2Kd: 40000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.084α = 90.00
b = 58.351β = 90.00
c = 66.891γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-12-08 
  • Released Date: 2012-02-08 
  • Deposition Author(s): Newman, J., Peat, T.S.

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references, Other
  • Version 1.2: 2014-02-05
    Type: Database references