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PDBsum entry 4abd

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protein ligands metals links
Hydrolase PDB id
4abd
Jmol PyMol
Contents
Protein chain
223 a.a.
Ligands
SO4 ×3
EDO ×2
SW2
DMS
Metals
_CA
Waters ×299
PDB id:
4abd
Name: Hydrolase
Title: Fragments bound to bovine trypsin for the sampl challenge
Structure: Cationic trypsin. Chain: a. Synonym: beta-trypsin, alpha-trypsin chain 1, alpha-trypsin ec: 3.4.21.4
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Other_details: sigma
Resolution:
1.25Å     R-factor:   0.146     R-free:   0.164
Authors: J.Newman,T.S.Peat
Key ref: J.Newman et al. (2012). The DINGO dataset: a comprehensive set of data for the SAMPL challenge. J Comput Aided Mol Des, 26, 497-503. PubMed id: 22187139
Date:
08-Dec-11     Release date:   08-Feb-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00760  (TRY1_BOVIN) -  Cationic trypsin
Seq:
Struc:
246 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.4  - Trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     digestion   2 terms 
  Biochemical function     protein binding     6 terms  

 

 
J Comput Aided Mol Des 26:497-503 (2012)
PubMed id: 22187139  
 
 
The DINGO dataset: a comprehensive set of data for the SAMPL challenge.
J.Newman, O.Dolezal, V.Fazio, T.Caradoc-Davies, T.S.Peat.
 
  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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