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PDBe Cheatsheet
Getting started with PDBe
Home page: http://www.ebi.ac.uk/pdbe/
►Tutorials on services are found under the 'Education' tab.
►Look for particular services under the 'PDBe services' sub-tab.
►Useful minitutorials are associated with 'QUIPS' articles.
►Quips homepage: http://www.ebi.ac.uk/pdbe-apps/quips
Some Jargon explained
PDB entries are named with four letters such
as '3o1u' shown here schematically (Fig. 1).
Entries contain the mean x,y,z coordinates of
modelled atoms. For X-ray structures they
also include Atomic Displacement
Parameters (ADPs – also called B-factors)
which indicate displacements of the atoms
from their mean coordinate position.
Fig. 1
Macromolecular polymers and small
oligomers are 'CHAINS' indicated by single
letter identifiers. One for each polymer – in
this example protein (chain A, red) and two strands of DNA (chain B, blue
and chain C, green). Water molecules (if modelled, shown all as red dots
here) get the same CHAIN letter as the nearest polymer.
Polymer CHAINS are made from RESIDUES which all get a three-letter code
– such as 'GLY', 'ALA', or for nucleotides ' A' – which start with two spaces
(highlighted as a grey box here). Residues are numbered in sequence
through each polymer – but this numbering scheme may not match UniProt
numbering!
►You can check the match for any UniProt using the
MDV
UniPDB service
http://www.ebi.ac.uk/pdbe-apps/widgets/unipdb
Drugs, metals, and small molecules are called
HETGROUPs or LIGANDS and also get a residue code
and the CHAIN letter of the closest polymer. For
example 3o1u contains the nucleotide MDV (Fig. 2).
Fig. 2
Try exploring the information for 3o1u – type this code into the search bar on
the PDBe home page and browse its Summary page.