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2 words
N ligand Notch ligand
 
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Methods and resources for obtaining chemically plausible starting models and restraint sets for refinement of ligand complexes are described and some of the potential pitfalls are discussed.

Gerard J. Kleywegt

Acta Crystallographica Section D: Biological Crystallography 63 (Pt 1), 01 Jan 2007

A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed. refinement model building ligand complexes restraint sets macromolecular crystallography Crystallography of complexes 1.

Gerard J. Kleywegt

Acta Crystallographica Section D: Biological Crystallography 63 (Pt 1), 01 Jan 2007

In addition, as the examples below show, compounds (known and unknown) may undergo chemical reactions, ‘known’ compounds may turn out to be something completely different and sometimes a putative ligand simply does not bind or binds with too low an occupancy to give a clear feature in the electron density.

Gerard J. Kleywegt

Acta Crystallographica Section D: Biological Crystallography 63 (Pt 1), 01 Jan 2007

Depending on the nature of the small molecule and the environment inside the protein, a ligand may be reduced or oxidized ( e.g. sulfur- or metal-containing compounds), it may form dimers ( e.g. β-mercaptoethanol may dimerize to form 2-­hydroxyethyldisulfide), it may turn out to be an unexpected substrate or it may react with the protein or other components present in the crystal.

Gerard J. Kleywegt

Acta Crystallographica Section D: Biological Crystallography 63 (Pt 1), 01 Jan 2007

An interesting example of an unexpected reaction taking place in a crystal (albeit with an unusual amino acid rather than a ligand) was encountered in the structure determination of a methanogen methyltransferase, the first known protein to contain a copy of the 22nd naturally occurring amino acid, l -pyrrolysine (Hao et al. , 2002 ▶ ).

Gerard J. Kleywegt

Acta Crystallographica Section D: Biological Crystallography 63 (Pt 1), 01 Jan 2007

1531 further examples >>
Publications
 

Crystallographic refinement of ligand complexes

Gerard J. Kleywegt

Acta Crystallographica Section D: Biological Crystallography , 01 Jan 2007

Crystallization of protein–ligand complexes

Anne M. Hassell et al.

Acta Crystallographica Section D: Biological Crystallography , 01 Jan 2007

PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures

Jae-Min Shin et al.

Nucleic Acids Research , 01 Jan 2005

LIGAND: chemical database of enzyme reactions

Susumu Goto et al.

Nucleic Acids Research , 01 Jan 2000

LIGAND database for enzymes, compounds and reactions.

S Goto et al.

Nucleic Acids Research , 01 Jan 1999

Posttranslational regulation of Fas ligand function

Matthias Voss et al.

Cell Communication and Signaling : CCS , 29 Dec 2008

Ligand recognition determinants of guanine riboswitches

Jérôme Mulhbacher et al.

Nucleic Acids Research , 01 Aug 2007

Assessment of automatic ligand building in ARP / wARP

Guillaume X. Evrard et al.

Acta Crystallographica Section D: Biological Crystallography , 01 Jan 2007

The Ligand Gated Ion Channel Database.

N Le Novère et al.

Nucleic Acids Research , 01 Jan 1999

LIGAND: database of chemical compounds and reactions in biological pathways

Susumu Goto et al.

Nucleic Acids Research , 01 Jan 2002

1526 further publications >>