“CHOODRAW”—an interactive molecular graphics program (PC/XT/AT) to display small molecules complexed with protein fragments selected from the protein data bank

Background: Despite the fact that lithium is not a biologically essential metallic element, its pharmacological properties are well known and human exposure to lithium is increasingly possible because of its used in aerospace industry and in batteries. Objective: Lithium-protein interactions are therefore interesting and the surveys of the structures of lithium-protein complexes is described in this paper. Methods: A high quality non-redundant set of lithium containing protein crystal structures was extracted from the Protein Data Bank and the stereochemistry of the lithium first coordination sphere was examined in detail. Results: Four main observations were reported: (i) lithium interacts preferably with oxygen atoms; (ii) preferably with side-chain atoms; (iii) preferably with Asp or Glu carboxylates; (iv) the coordination number tends to be four with stereochemical parameters similar to those observed in small molecules containing lithium. Conclusion: Although structural information on lithium-protein, available from the Protein Data Bank, is relatively scarce, these trends appears to be so clear that one may suppose that they will be confirmed by further data that will join the Protein Data Bank in the future.

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Finding enzyme cofactors in Protein Data Bank

Bioinformatics ◽

10.1093/bioinformatics/btz115 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3510-3511 ◽

Cited By ~ 3

Author(s):

Abhik Mukhopadhyay ◽

Neera Borkakoti ◽

Lukáš Pravda ◽

Jonathan D Tyzack ◽

Janet M Thornton ◽

...

Keyword(s):

Small Molecules ◽

Protein Data Bank ◽

Data Bank ◽

Supplementary Information ◽

Supplementary Data ◽

Release Process ◽

Enzyme Reactions ◽

Enzyme Cofactors ◽

Rest Api ◽

The Individual

Abstract Motivation Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains >67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them. Results The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process. Availability and implementation Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org/api). Supplementary information Supplementary data are available at Bioinformatics online.

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PDBe: improved findability of macromolecular structure data in the PDB

Nucleic Acids Research ◽

10.1093/nar/gkz990 ◽

2019 ◽

Cited By ~ 4

Author(s):

David R Armstrong ◽

John M Berrisford ◽

Matthew J Conroy ◽

Aleksandras Gutmanas ◽

Stephen Anyango ◽

...

Keyword(s):

Small Molecules ◽

Protein Data Bank ◽

Structure Data ◽

Data Access ◽

Data Bank ◽

Macromolecular Structure ◽

Rna Structures ◽

Founding Member ◽

Advanced Search ◽

Search Facility

Abstract The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.

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