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Protein Data Bank in Europe (PDBe)

Cristian Escobar

Scientific Database Curator

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Summary of this session�

  • Type of data available in the PDB.

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  • Functional data added to PDB entries.

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  • Why use PDBe APIs?

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  • Type of APIs available from PDBe.

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  • Examples of API usage.

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  • Other resources to learn more about PDBe APIs.

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  • Hands-on session.

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The Protein Data Bank (PDB) is an archive of� experimentally determined 3-dimensional structures of biological macromolecules���

Proteins

DNA/RNA

Bound ligands

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Worldwide Protein Data Bank (wwPDB)

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Worldwide Protein Data Bank (wwPDB)

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PDB

code

Experimental

Model

Experimental data

Entry annotation

Model and validation report distribution

Deposit

in the

PDB

Described in a paper

(or maybe not published)

Referenced in a paper

A “PDB code” refers to a structure

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~1%: Fibre diffraction, Neutron Crystallography, Solid state NMR

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Method

Total

2020

2021

2022

2023

2024

X-ray Crystallography

85%

84%

80%

74%

69%

66%

Solution NMR Spectroscopy

6.7%

3.3%

2.7%

2.9%

2.1%

2.0%

Electron Microscopy

8.4%

13%

17%

24%

29%

32%

236371 structures deposited until 27th May 2025

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  • Data added through deposition.

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  • Data provided by depositors or added during annotation.

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  • Data added to define experimental method, sequence information, validation and more …

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  • This information is added to the mmCIF file.

Metadata gives scientific meaning to coordinates

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SIFTS – Structure Integration with Function, Taxonomy and Sequence

Linking structures with sequences

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PDBe.org/2yi7

Press to visualize the model

File download:

mmCIF, PDB, validation report and other.

Structural analysis and macromolecule annotation

Entry title and citation

Macromolecule fuanctional role

Experimental data and validation

Ligands present in the model

Experimental method info

PDBe entry page example

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PDBe-KB: adding more functional data

  • PDBe-KB is a consortium of 34 data recourses that contribute annotations:

- Protein and domain annotation.

- Evolutionary conserved sites.

- Small molecules.

- Mutations and variations.

- Protein binding sites.

- Biophysical parameters.

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  • Combined with SIFTS, increases value of PDB data.

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PDBe-KB pages

PDBe.org

Structural context for a given protein:

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Example: UniProt P22303�  

https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/P22303

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PDBe-KB page for UniProt P22303

PDBe.org

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PDBe APIs

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Why use PDBe APIs?

PDBe.org

  • Large scale data analysis.

- Programmatic access allows access to this data.

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  • A protein entity can have multiple structures.

- Models with different ligands.

- Different experimental conditions.

- In complex with other macromolecules

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                  • Repetition of analysis task.

- Use different inputs.

- Repeat analysis as the data base grows.

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Getting started with PDBe APIs

PDBe.org

API ‘start page’:

Visit: https://www.ebi.ac.uk/pdbe/pdbe-rest-api

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Getting started with PDBe APIs

PDBe.org

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Example: querying using programmatic access

PDBe.org

https://www.ebi.ac.uk/pdbe/pdbe-rest-api

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PDBe.org

  • The documentation provides a list of fields which are available for querying.

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  • For example:

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pdb_id : PDB entry id code

Field name

Description of provided information

Example: querying using programmatic access

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Example: querying using programmatic access

PDBe.org

q=molecule_name:"Acetylcholinesterase"+q_organism_name:"homo sapiens"&

fl=pdb_id,resolution,release_year&

wt=json

  • Input box for an interactive query too.

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  • Basic query structure:

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Query (‘q=‘), Field list (‘fl=‘), output format (‘wt=‘, JSON as default)

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PDBe.org

  • Input box for an interactive query tool.

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Example: querying using programmatic access

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PDBe.org

Other sources of information about PDBe APIs

  • Programmatic access webinar series

- Six part series ranging from basics in PDBe programmatic access to advanced visualisation

- Visit pdbeurope.github.io/api-webinars for videos and tutorials

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  • API ‘start page’:

- Visit: https://www.ebi.ac.uk/pdbe/pdbe-rest-api

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PDBe.org

  • PDBe APIs training repository:

https://github.com/PDBeurope/pdbe-api-training/

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Other sources of information about PDBe APIs

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Hands-on session

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PDBe.org

Thank you for your attention!

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Any questions?

 pdbhelp@ebi.ac.uk

proteindatabank

@PDBeurope

 proteindatabank

pdbeurope

pdbart