- Course overview
- Search within this course
- What is PDBe?
- Why do we need PDBe?
- When to use PDBe?
- How to access and navigate PDBe?
- How to search the PDB using PDBe?
- Guided exercise 1: Giardia lamlia
- Exercise 1: How do I search PDB for Giardia lamblia?
- Exercise 1: How many proteins are there in the PDB for Giardia lamblia?
- Exercise 1: How many of these proteins function as enzymes?
- Exercise 1: Which part of the cell do these proteins come from?
- Exercise 1: What type of ligands do they interact with?
- Guided exercise 2: Glycolysis process
- Exercise 2: How do I search the PDB for enzymes involved in glycolysis?
- Exercise 2: Are all the 10 enzyme structures that are involved in the glycolytic pathway present in the PDB?
- Exercise 2: What part of the cell do the enzymes belong to?
- Exercise 2: How do I identify the different classes of enzymes (e.g. hydrolase) that participate in glycolysis?
- Exercise 2: How many of them display nucleotide binding activity?
- Exercise 2: Which protein family/families does the enzyme Glucokinase belong to?
- Exercise 2: How do I identify the best representative structure from each of the protein families?
- Exploring a PDB entry
- Summary
- Test your knowledge
- Your feedback
- Learn more
- Get help and support on PDBe
- References
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Get help and support on PDBe
EMBL-EBI’s PDBe Team develops and maintains the EBI’s Protein Data Bank in Europe.
Support
- Try the PDBe tutorials to find out more about macromolecular structures and how to navigate the PDBe website.
- For general enquiries about the PDB, email the PDB help desk.
- For deposition enquiries, email the PDB deposition or Electron Microscopy Data Bank deposition addresses.
- For general enquiries about the Electron Microscopy Data Bank, email the EMDB help desk.
Collaborators
PDBe collaborates with the X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy and cryo-Electron Microscopy (EM) communities. To keep abreast of new developments in the NMR community, PDBe has participated in EU projects and continues to contribute to the Collaborative Computational Project for the NMR community (CCPN). PDBe collaborates with EMDB, the international repository for electron volume maps, which are created using high-resolution biological transmission electron microscopy. EMDB contains both macromolecular images and structures reconstructed using the single-particle method and images of sub-cellular regions from electron tomography. PDBe also collaborates with RCSB and BMRB.
Funding
Core support for PDBe is provided by the European Molecular Biology Laboratory and The Wellcome Trust. Specific projects are funded by the European Union, the UK Biotechnology and Biosciences Research Council(BBSRC) and the National Institutes of Health (NIH).