PDBsum
Encyclopedia
PDBsum is database that provides an overview of the contents of each 3D macromolecular
structure deposited in the Protein Data Bank
.
Each structure in the PDBsum database includes an image of structure, molecular components contained in the complex, enzyme reaction diagram if appropriate, Gene Ontology
functional assignments, a 1D sequence annotated by Pfam
and InterPro
domain assignments, description of bound molecules and graphic showing interactions between protein and secondary structure, schematic diagrams of protein-protein interaction
s, analysis of clefts contained within the structure and links to external databases.
Macromolecule
A macromolecule is a very large molecule commonly created by some form of polymerization. In biochemistry, the term is applied to the four conventional biopolymers , as well as non-polymeric molecules with large molecular mass such as macrocycles...
structure deposited in the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
.
Each structure in the PDBsum database includes an image of structure, molecular components contained in the complex, enzyme reaction diagram if appropriate, Gene Ontology
Gene Ontology
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
functional assignments, a 1D sequence annotated by Pfam
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
and InterPro
InterPro
InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them....
domain assignments, description of bound molecules and graphic showing interactions between protein and secondary structure, schematic diagrams of protein-protein interaction
Protein-protein interaction
Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...
s, analysis of clefts contained within the structure and links to external databases.
See also
- Crystallographic databaseCrystallographic databaseA crystallographic database is a database specifically designed to store information about crystals and crystal structures. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology,...
- Protein structureProtein structureProteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
- Protein structure databasesProtein structure databasesIn biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data...