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PDBsum   Pictorial database of 3D structures in the Protein Data Bank

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 the interactions between them.         Read more ...

 

PDB code  (4 chars)    Example: "1kfv"

Text search 
Scans all TITLE, HEADER, COMPND, SOURCE and AUTHOR records in the PDB (eg to find a given protein by name).

Search by sequence

Perform FASTA search vs all sequences in the PDB to get a list of the closest matches.


Search by  
UniProt id:
(eg P03023, LACI_ECOLI, etc)
Pfam id:
(eg PF07992)
Ensembl id:
(eg ENSG00000086205, ENST00000256999)

Notes

* Enlarged versions of the Pfam domain diagrams on each entry's page can now be obtained via the + icon.
* A search for PDB structures by Ensembl gene/transcript identifier (ENSG/ENST) has been added to UniProt and Pfam searches above.
* Human variation data from the 1,000 Genomes Project is now included on the 'protein' pages of human proteins, showing where in the protein the natural variations occur (eg 3bfx).
* You can use the Generate option on the left to submit your own structure and get a password protected PDBsum analysis generated for it.

PDBsum in-house

PDBsumProprietary: For companies wishing to have PDBsum processing and display in-house for their proprietary structures (from x-ray crystallography, NMR spectroscopy, homology modelling or docking predictions) there is the opportunity to license the PDBsum pipeline software. For more details, please contact Dr Mark Swindells of EBISU at mark.swindells@ebisu.co.uk.

 

 

The development of PDBsum has been partly funded by the Wellcome Trust spacer

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Contents
PDBsum contains
107,716 entries, including
2,135 superseded
Last update: 26 October, 2014

In-house version

PDBsumProp
In-house version for companies to process own structures (see below left)

Related databases

EC->PDB
Enzyme 3D structures organized by the E.C. numbering hierarchy.

DrugPort
Structures of drugs and their target proteins in the PDB.

SAS
Searches sequence against all PDB sequences and structurally annotates alignment.

ProFunc
Prediction of protein function from 3D structure.

ArchSchema
Graphs of protein sequences having related Pfam domain architectures.