PDB Archive Downloads


Please note that the FTP file download protocol in the PDB archive has been deprecated since November 1st 2024 (announcement).

The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.

wwPDB: https://files.wwpdb.org, rsync://rsync.wwpdb.org
RCSB PDB (US): https://files.rcsb.org, rsync://rsync.rcsb.org (see the download protocol below)
PDBe (UK): ftp.ebi.ac.uk/pub/databases/pdb/
PDBj (Japan): ftp://ftp.pdbj.org, https://files.pdbj.org, rsync://rsync.pdbj.org

The PDB versioned sites (See announcement) are updated the same time when the main archive sites are updated.

wwPDB: https://files-versioned.wwpdb.org, rsync://rsync-versioned.wwpdb.org
RCSB PDB (US): 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.

Data types File formats Location
Atomic coordinates PDBx/mmCIF, XML, and PDB https://files.wwpdb.org/pub/pdb/data/structures/
X-ray data: Structure Factors PDBx/mmCIF https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/
NMR data: Restraints and chemical shifts NEF (/nmr_data), NMR-STAR, and native refinement program formats https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/
https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/
https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints/
https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/
Small molecules references: CCD and BIRD PDBx/mmCIF https://files.wwpdb.org/pub/pdb/refdata/chem_comp/
https://files.wwpdb.org/pub/pdb/refdata/bird
Assemblies PDBx/mmCIF, PDB https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/
https://files.wwpdb.org/pub/pdb/data/biounit/PDB/
Archive holdings JSON https://files.wwpdb.org/pub/pdb/holdings/

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.

RCSB PDB:

Using http protocol:

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

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

Need further help with the US site: Please contact info@rcsb.org if you have any problems with file download.

PDBe:

Using http protocol:

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

Access 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

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. Use the user 'anonymous' when prompted. Alternatively, use lftp as below 

lftp http://ftp.ebi.ac.uk

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 http protocol:

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/

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.

Need further help with the PDBj site: Please contact PDBj https://pdbj.org/contact if you have any problems connecting to ftp.pdbj.org

Archive Snapshots

The annual archive snapshots provide the data in the archive at the start of each year or at selected milestone moments. These data may be used to provide a stable set of entries for analysis and allow users to see changes introduced due to remediation efforts by wwPDB.

Access to these snapshots is available through HTTP, rsync, FTP, and AWS sync protocols.

HTTP Protocol

RCSB PDB (US/AWS): https://s3snapshots.rcsb.org

PDBj (Japan): https://snapshots.pdbj.org

RSYNC Protocol

PDBj (Japan): rsync -avy snapshots.pdbj.org:: .

FTP Protocol

PDBj (Japan): ftp://snapshots.pdbj.org

AWS SYNC Protocol

RCSB PDB (US/AWS): s3://pdbsnapshots/

AWS SYNC Instruction:

  1. Install AWS CLI tool

    • List all PDB Snapshot objects

    • aws s3 ls s3://pdbsnapshots/ --no-sign-request

    • When you see a result like:

    • 20250101/ PRE 20250101/
      • PRE: This indicates that the listed item is a "prefix" or "folder" in the S3 bucket, not a file object. This is how S3 organizes files logically into folders.
      • 20250101/: This is the prefix (or "folder") in the S3 bucket. It's not an actual folder in the traditional sense, but rather a common prefix used to group objects.

    • Sync PDB Snapshots

    • All PDB Snapshot objects

    • aws s3 sync s3://pdbsnapshots/ ./local-directory/ --no-sign-request

    • Specific PDB snapshot object (e.g., /20250101)

    • aws s3 sync s3://pdbsnapshots/20250101/ ./local-directory/20250101 --no-sign-request