As large structures (containing >62 chains and/or 99999 ATOM lines) cannot be represented in the legacy PDB file format, data are available in the PDB archive as:
Single PDBx/mmCIF files that represent the entire structure. The single PDBx/mmCIF files are available from each Structure Summary page on the RCSB PDB website and from the FTP archive (in directories of the format ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/bc/abcd.cif.gz).
TAR files containing a collection of best effort/minimal files in the PDB file format to support users and software tools that rely solely on the PDB file format. The entire structure is divided into several minimal files. The TAR files are available for download from each Structure Summary page and in a separate directory in the PDB FTP archive (ftp://ftp.wwpdb.org/pub/pdb/compatible/pdb_bundle/) grouped by the middle two characters of the 4-character PDB ID.
Best effort/minimal PDB format files contain only authorship, citation details and coordinate data under HEADER, AUTHOR, JRNL, CRYST1, SCALEn, ATOM, HETATM records.
The following PDB records are not included in the best effort/minimal files: OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, REVDAT, SPRSDE, REMARKS, DBREF, SEQADV, SEQRES, MODRES, HET, HETNAM, HETSYN, FORMUL, HELIX, SHEET, SSBOND, LINK, CISPEP, SITE, ORIGXn, MTRIXn, CONECT.
Example: Truncated best effort/minimal file for the entry 4u50
HEADER RIBOSOME 2014-07-24 XXXX AUTHOR N.GARREAU DE LOUBRESSE, I.PROKHOROVA, G.YUSUPOVA, M.YUSUPOV JRNL AUTH N.Garreau de Loubresse, I.Prokhorova, W.Holtkamp, JRNL AUTH 2 M.V.Rodnina, G.Yusupova, M.Yusupov JRNL TITL Structural basis for the inhibition of the eukaryotic JRNL TITL 2 ribosome. JRNL REF Nature V. 513 517 2014 JRNL REFN NATUAS UK 1476-4687 JRNL PMID 25209664 JRNL DOI 10.1038/nature13737 CRYST1 434.390 285.580 303.060 90.00 98.99 90.00 P 1 21 1 4 SCALE1 0.002302 0.000000 0.000364 0.00000 SCALE2 0.000000 0.003502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003341 0.00000 ATOM 1 P U A 1 -88.608 31.952 64.746 1.00 81.64 P ANISOU 1 P U A 1 5964 13260 11795 1046 -383 -1793 P ATOM 2 OP1 U A 1 -88.681 32.341 63.314 1.00 82.66 O ANISOU 2 OP1 U A 1 6111 13412 11886 1075 -507 -1778 O ...
The TAR file also contains an index file with the mapping between the chains present in the large entry and the chains present in the minimal PDB format files.
Example: Truncated index file for the entry 4u50
New chain ID Original chain ID 4u50-pdb-bundle1.pdb: A 2 B S0 C S1 D S2 ...
- An index of all large structure entries (that do not have a standard PDB format file) is updated regularly on the PDB FTP site at ftp://ftp.wwpdb.org/pub/pdb/compatible/pdb_bundle/pdb_bundle_index.txt. This list will continue to grow as new large structures are deposited and released. These entries can also be selected using Advanced Search (under Structure Annotation > Large Structures)
Historically, these large files were "split" across multiple PDB format files. These files were combined into single entries at the end of 2014 (wwPDB Announcement). An index file mapping large structures to corresponding obsoleted split entries is available at ftp://ftp.wwpdb.org/pub/pdb/compatible/pdb_bundle/large_split_mapping.tsv. This file does not list large structures that were never deposited as split entries.