PDBx/mmCIF FAQ
PDB entries in PDBx/mmCIF format are stored on the ftp sites of the wwPDB partners at one of the locations:
Entries containing very large structures stored PDBx/mmCIF format are currently stored separately one of the locations:
- ftp for large PDBx/mmCIF at RCSB PDB
- ftp for large PDBx/mmCIF at PDBe
- ftp for large PDBx/mmCIF at PDBj
The PDB structure entry files in PDBx/mmCIF format are named following the convention <PDB_4-LETTER-ID_CODE>:.cif.gz (e.g. 1abc.ent.gz).
Experimental data files containing X-ray structure factors are only distributed in PDBx/mmCIF format and are named following an
older PDB naming convention r<PDB_ID_CODE>:.ent.gz (e.g. r1abc.ent.gz).
A complete description of the download options for PDB data files is maintained at here by the wwPDB. The special handling of PDB entries containing very large structures is available here.
The PDBx/mmCIF format has a simple appearence with only a few syntax elements. All of syntax elements used in PDB data files are shown in the following snippet describing polymer sequence.
The essential syntax features include:
- All data items are identified by name and begin with the underscore character,
_entity_poly.entity_id. - Data item names can be decomposed into a category name and an attribute name,
_category.attributewhich are separated by a period. - Data categories are presented in two styles: key-value and tabular. In the example, categories
entity_name_comandentity_polyboth use the key-value style and theentity_poly_seqcategory uses the tabular style. In the tabular sytle, the data item names correpsonding to the table columns follow a reservedloop_token which are followed by the rows of data rows of white-space delimited data values. - Any character data value may be quoted using encapsulating single or double quotes; however, character values containing
internal whitespace (e.g. the value of
_entity_name_com.name) must be quoted. Character values that extend over multiple lines are quoted using leading and trailing semi-colons positioned at the first character position of the records surronding the multi-line character value (e.g._entity_poly.pdbx_seq_one_letter_code). - Lines beginning with the hash symbol
#are comments.
Look here for a more complete description of PDBx/mmCIF data file and dictionary syntax.
# <-- a comment line _entity_name_com.entity_id 1 _entity_name_com.name "Pantoate--beta-alanine ligase, Pantoate-activating enzyme" _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;AMAIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDL DAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGE KDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVL DAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTFAGTDRPDGYR ; # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ALA n 1 2 MET n 1 3 ALA n 1 4 ILE n 1 5 PRO n 1 6 ALA n 1 7 PHE n # .... abbreviated ....