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.
Also included are the AlphaFold predicted models for all human protein for comparison with experimentally determined structures. Read more ...

Enter UniProt accession (or UniProt id), to find Alpha Fold model of given protein. Eg P00734 (THRB_HUMAN).

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

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

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COVID-19 structures

The SARS-CoV-2 virus genome has 14 open reading frames coding for at least 29 protein: four structural proteins, making the outer coat and its characteristic protruding spikes, sixteen or more non-structural proteins involved in the virus's replication, and nine accessory proteins that are thought to counteract the host's immune response.

Many of the proteins have been structurally determined and deposited in the PDB. Three examples are shown below.

For the full list, go to COVID-19 protein structures

Spike protein. The spikes on the surface of the virus bind to specific host cell receptors and initiate cell infection. The structure shows a trimeric complex of the spike glycoprotein (in its closed state).
PDB entry 6vxx
Pubmed ref 32155444

Main protease responsible for cleaving the main polyprotein into its separate non-structural proteins, here shown with a bound inhibitor.
PDB entry 5r81

RNA-binding domain of the nucleocapsid phosphoprotein. Tetrameric complex of N-terminal domains of the protein which is a facilitator for reverse transcription and integration.
PDB entry 6vyo

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

Contents

PDBsum contains
206,449 entries, including
1,781 superseded
Last update: 10 April, 2023

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Searches sequence against all PDB sequences and structurally annotates alignment.

Prediction of protein function from 3D structure.

Graphs of protein sequences having related Pfam domain architectures.