Depositing Structures with Ligands

03/08

(Click image to enlarge)
Ligand Expo can also be used to check and confirm the chemistry of a chemical component. Shown is the correct sterochemistry for alpha-D-mannose (on the left, ID: MAN) and for N-acetyl-D-glucosamine (on the right, ID: NAG).

Ligand Expo (ligand-expo.rcsb.org) accesses chemical and structural information about all small molecule components found in PDB entries. It is based upon the Chemical Component Dictionary maintained by the wwPDB.

When depositing a structure with a ligand

• Search Ligand Expo for a chemical component that matches your ligand
• If a match is found, use the corresponding three-character code for the ligand in your coordinates
• If the ligand is new, choose a new three-character code for the ligand.
• When depositing your structure with ADIT, upload the chemical name and formula and/or a file showing the chemical image for the new ligand into the Ligand Information section

Ligand Expo can search the Chemical Component Dictionary using uploaded data files (e.g., PDB, MOL/SDF, Refmac/Phenix monomer library (mmCIF)); chemical name; formula; SMILES string; and ID code.

Searches for instances of ligands associated with macromolecular structures can also be performed at www.pdb.org using a variety of options, including the top bar Chemical Name/ID search, Advanced Search, and the Chemical Structure Search. Users can then explore the ligand structures and the related PDB entries. Online screencasts are available at the RCSB PDB site to help users explore these features.

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