ISDA

Deposition Date 2011-12-08

Release Date 2012-02-08

Last Version Date 2024-11-06

Entry Detail

PDB ID:

4AB8

Keywords:

HYDROLASE

Title:

Fragments bound to bovine trypsin for the SAMPL challenge

Biological Source:

Source Organism:

BOS TAURUS (Taxon ID: 9913)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.60 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.17

Space Group:

P 31 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CATIONIC TRYPSIN
Gene (Uniprot):PRSS1
Chain IDs:A
Chain Length:223
Number of Molecules:1
Biological Source:BOS TAURUS

UniProt ID:P00760 Pfam ID:PF00089 EC:3.4.21.4

Ligand Molecules

EDO

SO4

VXU

Primary Citation

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

Newman, J, Dolezal, O, Fazio, V, Caradoc-Davies, T, Peat, T.S, Newman, J, Fazio, V.J, Caradoc-Davies, T.T, Branson, K, Peat, T.S, Dolezal, O, Doughty, L, Hattarki, M.K, Fazio, V.J, Caradoc-Davies, T.T, Newman, J, Peat, T.S.Show

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

PMID: 22187139 DOI: 10.1007/S10822-011-9521-2

Abstact

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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Protein

Chemical

Disease

Primary Citation of related structures