PDB Archive Downloads

New Sequence and InChI
Data Structure and Content
Download Protocols

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

wwPDB: ftp://ftp.wwpdb.org, https://files.wwpdb.org, rsync://rsync.wwpdb.org
RCSB PDB (US): ftp://ftp.rcsb.org, https://files.rcsb.org, rsync://rsync.rcsb.org (see the download protocol below)
RCSB PDB (US/AWS): https://s3.rcsb.org
PDBe (UK): ftp.ebi.ac.uk/pub/databases/pdb/
PDBj (Japan): ftp.pdbj.org

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/

New Sequence and InChI

Every Saturday by 3:00 UTC, for every ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/ew entry, the wwPDB website provides: sequence(s) (amino acid or nucleotide) for each distinct polymer (new_release_structure_sequence.tsv) and, where appropriate, the InChI string(s) for each distinct ligand (new_release_structure_nonpolymer.tsv) and the crystallization pH value(s) (new_release_crystallization_pH.tsv).

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.

all_removed_entries.json.gz List of removed PDB entries (obsolete, models) with entry authors, entry title, release date, obsolete date , and superseding PDB ID, if any.
current_file_holdings.json.gz List of released PDB entries and file types present for each entry in the PDB Core Archive (e.g., coordinate data, experimental data, validation report, ...)
obsolete_structures_last_modified_dates.json.gz List of obsolete PDB entries with last time of PDBx/mmCIF file modification
refdata_id_list.json.gz List of released chemical reference entries, content types (e.g., Chemical Component, BIRD), and last time of reference file modification
released_structures_last_modified_dates.json.gz List of released PDB entries with last time of PDBx/mmCIF file modification
unreleased_entries.json.gz List of on-hold PDB entries, entry status, deposition date, and sequence pre-release information

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 ftp.pdbj.org