PDB Archive Downloads
New Sequence and InChI
Data Structure and Content
Download Protocols
Please note that the FTP file download protocol in the PDB archive will be deprecated on November 1st 2024 (announcement).
The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.
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RCSB PDB (US): ftp://ftp.rcsb.org, https://files.rcsb.org, rsync://rsync.rcsb.org (see the download protocol below)
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The versioned FTP sites (See announcement) are updated the same time when the main FTP sites are updated.
wwPDB: ftp://ftp-versioned.wwpdb.org, https://files-versioned.wwpdb.org, rsync://rsync-versioned.wwpdb.org
RCSB PDB (US): ftp://ftp-versioned.rcsb.org/, https://files-versioned.rcsb.org, rsync://rsync-versioned.rcsb.org
PDBe (UK): ftp://ftp.ebi.ac.uk/pub/databases/pdb_versioned/
PDBj (Japan): ftp://ftp-versioned.pdbj.org/, https://files-versioned.pdbj.org, rsync://rsync-versioned.pdbj.org
New Sequence and InChI
Every Saturday by 3:00 UTC, for every new entry the wwPDB website provides:
Data Structure and Content
Primary data (atomic coordinates and experimental data) are stored using a hash directory.
List of archive holdings
These inventory data files at /pub/pdb/holdings/ offer a quick overview of data in the archive.
current_file_holdings.json.gz |
a list of released PDB entries and the file types present for each in the PDB Core Archive (e.g. coordinate data, experimental data, validation report). |
refdata_id_list.json.gz |
a list of released chemical reference entries, their content types (e.g., Chemical Component, BIRD), and the most recent modification date of the reference file. |
released_structures_last_modified_dates.json.gz |
a list of released PDB entries with the most recent modification date of the PDBx/mmCIF file. |
released_experimental_data_last_modified_dates.json.gz |
a list of released experimental data files with the most recent modification date. |
obsolete_structures_last_modified_dates.json.gz |
a list of obsoleted PDB entries with the most recent modification date of the PDBx/mmCIF file. |
obsolete_experimental_data_last_modified_dates.json.gz |
a list of obsoleted experimental data files with the most recent modification date. |
all_removed_entries.json.gz |
a list of obsoleted PDB entries including information for entry authors, entry title, release date, obsolete date, and superseding PDB ID, if any. |
unreleased_entries.json.gz |
a list of on-hold PDB entries, their entry status, deposition date, and pre-release sequence information, where available. |
Download Protocols
Every Wednesday from 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB repository sites. The PDB archive is quite large, requiring over 1TB of storage, and continues to grow with each weekly update.
All files mentioned above are available via 3 different protocols: ftp, https and rsync. For individual file downloads we recommend https. The ftp protocol will be gradually phased out. For bulk file downloads we recommend rsync, see more instructions about rsync below.
Download instructions for: RCSB PDB (USA) |
PDBe (UK) | PDBj (Japan)
RCSB PDB:
Using rsync protocol:
rsync --port=33444 rsync.rcsb.org::
ftp Top level of PDB ftp tree ( /pub/pdb )
ftp_data Data directory within PDB ftp archive ( /pub/pdb/data )
ftp_derived Derived data directory within PDB ftp archive ( /pub/pdb/derived_data )
ftp_doc Doc directory within PDB ftp archive ( /pub/pdb/doc )
emdb Top level of EMDB ftp tree ( /pub/emdb )
Download coordinate files in PDB Exchange Format (mmCIF):
rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF
Download coordinate files in PDBML Format (xml):
rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::ftp_data/structures/divided/XML/ ./XML
Download coordinate files in PDB Format:
rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::ftp_data/structures/divided/pdb/ ./pdb
Download EMDB map metadata header files (xml):
rsync -rlpt -v -z --delete --port=33444 --include "emd-*.xml" \
"rsync.rcsb.org::emdb/structures/EMD-*/header/" ./header
Download directories/files for EMDB entry EMD-5001:
rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::emdb/structures/EMD-5001/ ./EMD-5001
Download the validation report files:
rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::ftp/validation_reports/ ./validation_reports
Download coordinate files in PDB Exchange Format (mmCIF):
https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF
Download coordinate files in PDBML format:
https://files.rcsb.org/pub/pdb/data/structures/divided/XML
Download coordinate files in PDB format:
https://files.rcsb.org/pub/pdb/data/structures/divided/pdb
Download EMDB data files:
https://files.rcsb.org/pub/emdb/structures
Download the validation report files:
https://files.rcsb.org/pub/pdb/validation_reports
Need further help with the US site: Please contact
info@rcsb.org if you have any problems connecting to ftp.rcsb.org.
PDBe:
Using rsync protocol:
rsync rsync.ebi.ac.uk:: pub ftp.ebi.ac.uk /pub area
Download coordinate files in PDB Exchange Format (mmCIF):
rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ \
./mmCIF
Download coordinate files in PDBML Format (xml):
rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/XML/ \
./XML
Download coordinate files in PDB Format:
rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/pdb/ \
./pdb
Download EMDB map metadata header files (xml):
rsync -rlpt -v -z --delete --include "emd-*.xml" \
"rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-*/header/" ./header
Download directories/files for EMDB entry EMD-1003:
rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-1003/ ./EMD-1003
Download the validation report files:
rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/pdb/validation_reports/ \
./validation_reports
Using ftp protocol:
ftp ftp.ebi.ac.uk
will connect to an anonymous ftp server containing the remediated wwPDB repository.
Download coordinate files in PDB Exchange Format (mmCIF):
https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF
Download coordinate files in PDBML format:
https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/XML
Download coordinate files in PDB format:
https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/pdb
Download the full PDB ftp tree:
https://ftp.ebi.ac.uk/pub/databases/pdb/
Download EMDB data files:
https://ftp.ebi.ac.uk/pub/databases/emdb/structures
Download the validation report files:
https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports
Need further help with the PDBe site: Please contact PDBe (http://www.ebi.ac.uk/pdbe/about/contact or e-mail
pdbehelp@ebi.ac.uk) if you have any problems connecting to ftp.ebi.ac.uk.
PDBj:
Using rsync protocol:
rsync ftp.pdbj.org::
ftp Top level of PDB ftp tree approximately ( /pub/pdb )
ftp_data Data directory within PDB ftp archive Approximately ( /pub/pdb/data )
ftp_derived Derived data directory within PDB ftp archive Approximately ( /pub/pdb/derived_data )
ftp_doc Doc directory within PDB ftp archive Approximately ( /pub/pdb/doc )
emdb Top level of EMDB ftp tree Approximately ( /pub/emdb )
rsync Top level of PDBj FTP tree aproximately ( / )
Download coordinate files in PDB Exchange Format (mmCIF):
rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF
Download coordinate files in PDBML Format (xml):
rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/XML/ ./XML
Download coordinate files in PDB Format:
rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/pdb/ ./pdb
Download EMDB map metadata header files (xml):
rsync -rlpt -v -z --delete --include "emd-*.xml" \
"ftp.pdbj.org::emdb/structures/EMD-*/header/" ./header
Download directories/files for EMDB entry EMD-5001:
rsync -rlpt -v -z --delete \
ftp.pdbj.org::emdb/structures/EMD-5001/ ./EMD-5001
Download the validation report files:
rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp/validation_reports/ ./validation_reports
Using ftp protocol:
ftp ftp.pdbj.org
will connect to an anonymous ftp server at PDBj containing the remediated wwPDB repository.
Download coordinate files in PDB Exchange Format (mmCIF):
https://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/
Download coordinate files in PDBML format (all):
https://ftp.pdbj.org/pub/pdb/data/structures/divided/XML/
Download coordinate files in PDBML format (no-atom site information):
https://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-noatom/
Download coordinate files in PDBML format (atom site information only):
https://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-extatom/
Download coordinate files in PDB format:
https://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/
Download EMDB data files:
https://ftp.pdbj.org/pub/emdb/structures
Download the validation report files:
https://ftp.pdbj.org/pub/pdb/validation_reports/
Need further help with the PDBj site: Please contact PDBj
https://pdbj.org/contact if you have any problems connecting to
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Archive Snapshots
RCSB PDB (US/AWS): https://s3snapshots.rcsb.org
PDBj (Japan): ftp://snapshots.pdbj.org