ADIT deposition tool | deposit your structures to the PDB

Tutorial | ADIT FAQ | Deposition FAQ | pdb_extract | Ligand Expo

NOTICE FOR REFMAC USERS - details for generating total B factors when TLS used

For structures solved by Electron Microscopy, first deposit the 3D map at EMDB and then follow the link provided to deposit the coordinates.

Note: Ligand and Water Chain ID and Numbering

During annotation, ligand and water molecule chain IDs will be changed to match that of adjacent polymers. Their numbering will start at the first multiple of 100 beyond the last polymer residue or ligand.

ADIT depositors can submit their sequences to serve as puzzle challenges for the Foldit community. For more information, see here.

If you are depositing a protein-protein, protein-DNA, protein-RNA or protein-peptide complex, you may consider submitting your structure as a target to CAPRI (Critical Assessment of Predicted Interactions) after depositing your entry to the PDB.

To start a new ADIT session, select the experimental method and the molecular structure type. Then press the BEGIN button.

New ADIT Session
Method:	X-ray NMR Electron Microscopy	Structure Type:	Protein Nucleic acid Nucleic acid/protein complex

To continue a session from an earlier date, enter your session restart ID and press the CONTINUE SESSION button.

Continue Previous ADIT Session*
Session Restart ID: example: 2006-07-01.serverhostname.9999.12345678
* ADIT-NMR sessions can be continued at http://deposit.bmrb.wisc.edu/bmrb-adit/

Detailed instructions that describe how to deposit X-ray, NMR and Electron Microscopy structures are available. Coordinates may be deposited as either mmCIF or PDB formatted files. To ensure that all tools will work with minimal error, the format requirements for depositing structures in PDB format are:

• Each polymer must be assigned a unique alphanumeric chain ID (A-Z, 0-9, a-z) in column 22.
• Each residue must be assigned a unique residue number within that chain ID.
• If there are alternate conformations in the structure, the alternate conformation indicator must be provided in column 17.
• Atoms with the same coordinates may not be present in the same MODEL.
• All polymer chains should have a TER card at the end. No TER cards should be included at the end of non-polymer residues (such as ions, ligands, waters).
• There should be only one END card at the end of the file.
• Each record must start in the first column.
• Record types (such as COMPND, ATOM, SEQRES) must be capitalized.
• If the entry contains ANISOU, SIGATM, or SIGUIJ lines, there must be a corresponding ATOM record.
• Depositions with multiple models should include MODEL and ENDMDL cards. The models should be listed sequentially in columns 11-14.
• Chain IDs used in the SEQRES records should correspond to those in the coordinates.
• The sf file can either be in mmCIF, ASCII, or mtz formats and should at least include h, k, l, F, SigmaF (and/or I and SigmaI) and test flags.
  Definitions and format are available in DOC (48 KB) and PDF (24 KB) format.

The guidelines for data processing and policies are available at http://www.wwpdb.org.

Question, Comments, and suggestions should be sent to deposit@deposit.rcsb.org.