Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.95 kDa 
• Atom Count: 2000 
• Residue Count: 223 
• Unique protein chains: 1

4AB8

Fragments bound to bovine trypsin for the SAMPL challenge

• DOI: 10.2210/pdb4AB8/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

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

• PubMed: 22187139 
• DOI: 10.1007/s10822-011-9521-2
• Structures With Same Primary Citation


• 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 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.

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Related Citations: 

• 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

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CATIONIC TRYPSIN	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VXU	A	3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine C10 H13 N O2 ZXJOKQNPRXXPJT-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
VXU	Kd :  136000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.323	α = 90
b = 54.323	β = 90
c = 105.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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: 2014-02-05
  Changes: Database references