 |
About PDBsum
Description
The PDBsum is a pictorial database that provides an at-a-glance
overview of the contents of each 3D structure deposited in the Protein
Data Bank (PDB).
It shows the molecule(s) that make up the structure (ie protein
chains, DNA, ligands and metal ions) and schematic diagrams of their
interactions. Extensive use is made of the freely available
RasMol, JSmol, and PyMOL molecular graphics
programs to view the molecules and their interactions in 3D.
A new addition is the inclusion of over 23,000 Alpha Fold predicted models for all human protein. These are coloured
by the confidencee in the accuracy of each part of the model, using the same
colouring scheme as on the Alpha Fold website.
Search
Entries are accessed either by their 4-character PDB code, or by
one of the two search boxes provided on the PDBsum home page:
- text search, which searches a given
string against the TITLE, HEADER, COMPND, SOURCE and AUTHOR records in the
PDB. For a fuller description of the options that the text search offers, see
here.
- sequence search, which performs a FASTA
search of a given protein sequence against the sequences of all proteins
in the PDB. The top hits are listed with links to their PDBsum pages.
Browse
You can also use any of the Browse options
given on the PDBsum home page:
- Highlights - which tabulates
some of the extreme structures in the database in terms of age, size, etc
- List of PDB codes - which lists
all entries by their 4-character code
- Het Groups - lists all Het Groups
in the PDB with links to the structures that contain them
- Ligands - as for Het Groups, but
considering each bound molecule as a separate entity (often consisting of
several covalently joined Het Groups)
- Drugs - lists the drug
molecules (and neutraceuticals) found in structures of the PDB.
- Enzymes - lists all enzyme structures
in the PDB classed by the hierarchical E.C. numbering scheme. Also known
as the Enzyme Structures Database or
EC->PDB
- ProSite - lists all PROSITE sequence
patterns and the PDB entries that contain them
- Pfam - lists the PDB entries
containing structural information for any Pfam domain
- Species - classifies all PDB
entries by the source species from which the protein comes
Information presented on the PDBsum pages
The information given on each PDBsum entry is spread across several
pages, as listed below and accessible from the tabs at the top of the page.
Only the relevant tabs will be present on any given page.
- Top page
- summary information including thumbnail image of structure, molecules in
structure, enzyme reaction diagram (where relevant), GO functional assignments,
and selected figures from key reference
- Protein
- wiring diagram, topology diagram(s) by CATH domain, and residue conservation
(where available)
- DNA/RNA
- DNA/RNA sequence and NUCPLOT showing interactions made with protein
- Ligands
- description of bound molecule and LIGPLOT showing interactions made with
protein
- Prot-prot
- schematic diagrams of any protein-protein interfaces and the residue-residue
interactions made across them
- Clefts
- listing of top ten clefts in the surface of the protein, listed by volume
with any bound ligands shown
- Links
- links to external databases
PDBsum publications
Latest reference
|
Laskowski R A, Thornton J M (2021).
PDBsum extras: SARS-CoV-2 and AlphaFold models.
Prot. Sci., 31, 283-289.
|
Earlier references
|
|
Laskowski R A, Jabłońska J, Pravda L, Vařeková R S, Thornton J M (2018).
PDBsum: Structural summaries of PDB entries.
Prot. Sci., 27, 129-134.
|
|
|
|
de Beer T A P, Berka K, Thornton J M, Laskowski R A (2014).
PDBsum additions.
Nucleic Acids Res., 42, D292-D296.
[PubMed id: ]
|
|
|
|
|
Laskowski R A (2009). PDBsum new things.
Nucleic Acids Res., 37, D355-D359.
[PubMed id: ]
|
|
|
|
|
Laskowski R A, Chistyakov V V, Thornton J M (2005). PDBsum more: new
summaries and analyses of the known 3D structures of proteins and
nucleic acids. Nucleic Acids Res., 33, D266-D268.
[PubMed id: ]
|
|
|
|
|
Laskowski R A (2001). PDBsum: summaries and analyses of PDB
structures. Nucleic Acids Res., 29, 221-222.
[PubMed id: ]
|
|
|
|
|
Laskowski R A, Hutchinson E G, Michie A D, Wallace A C, Jones M L,
Thornton J M (1997). PDBsum: A Web-based database of summaries and analyses
of all PDB structures. Trends Biochem. Sci., 22, 488-490.
[PubMed id: ]
|
Related reference
|
|
Laskowski R A (2007). Enhancing the functional annotation of PDB
structures in PDBsum using key figures extracted from the literature.
Bioinformatics, 23, 1824-1827.
[PubMed id: ]
|
|
|
Credits
The original version of PDBsum (c.1995) was created
by:
,
,
Alex Michie,
Andrew Wallace,
Martin Jones,
,
,
,
Atsushi Kasuya
and
at the
,
New version by:
and
at the
|