The Protein Feature View provides graphical summaries of
full-length protein sequences from UniProtKB
and how they relate to PDB
entries. The Protein Feature View loads annotations from external databases such as
domain annotations from SCOP
and SCOPe, and
regions for which homology models are available from the
SWISS-MODEL Repository. There are also
tracks available that
display predicted regions of protein disorder (computed with
and hydrophobic regions, computed using a sliding window approach.
Predicted disordered and hydrophobic regions are in red; ordered and
hydrophilic regions are in blue.
For human proteins that can be mapped to the human genome, a track describes the projection
of the protein structure onto the genome. ProteinFeatureView is currently available for all
SwissProt entries (also those without PDB structures), as well as the small subset of TREMBL entries
that can get linked to PDB.
By default, representative PDB entries are displayed to provide
an overview of
UniProtKB sequence regions that are included in PDB entries.
The view can be expanded by pressing the
"+" icon or by selecting the "Extended" menu
option to show all available PDB
entries (many, in some cases).
View An example Protein Feature View
The header section of the Protein Feature View displays information from
UniProtKB about the function, catalytic activity and subunit structure (if available) of the sequence.
The header section also contains an option to select Protein Feature Views from related organisms with the same gene name.
The Action button has an option to map sequence motifs in the Protein Feature View as shown below.
On Structure Summary pages, the Protein Feature View shows a track that provides a per-residue perspective of the wwPDB validation report.
The track uses color coding to indicate the number of bond angle outliers, bond length outliers, and clashes for a given residue.
Shown as an example below is one of the chains of PDB ID 4HHB, a structure of hemoglobin
originally released in 1984. As modern refinement and validation tools were not available in 1984, the validation track is mostly orange and red due to the presence
of a large number of geometric outliers.
By comparison, (see below) the validation track for one of the chains of the hemoglobin structure PDB ID 2W72,
which was released in 2009, shows many fewer geometric outliers, although it does have several residues that are poorly fit into the electron density (RSRZ>2)
For more details on wwPDB validation reports please see the wwPDB website or
read the article that describes the recommendations of the X-ray Validation Task Force.
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.