Welcome to the Worldwide Protein Data Bank

Access the PDB FTP:

RCSB PDB | PDBe | PDBj

Archive Download

Chemical Component Dictionary

Deposit Data to the PDB:

RCSB PDB | PDBe

PDBj | BMRB

Search for Structures:

RCSB PDB | PDBe

PDBj | BMRB

PDB Archive Snapshots:

RCSB PDB | PDBj

Instructions to Journals

Documentation

Format

Annotation and Policies

Remediation

Validation Reports

Workshops and Task Forces

X-ray Validation

NMR Validation

EM Validation

PDBx/mmCIF Working Group

PDB40

wwPDBAC

EMDB

Data Download Details

The wwPDB ftp site is quite large. As of March 7, 2012, it contains more than 610,000 files requiring over 186 GBbytes of storage. It will continue to grow with each weekly update. Fresh downloads will require substantial amount of time.

A number of download locations and options are provided to make access as efficient as possible.

Access is available from: the RCSB PDB (USA) | PDBe (UK) | PDBj (Japan)

Please note: ftp://ftp.rcsb.org is no longer updated. Please access the PDB archive using one of the FTP sites listed in the left menu.

RCSB PDB:

Using rsync protocol:

rsync --port=33444 ftp.wwpdb.org::

ftp            	Top level of PDB ftp tree approximately 130 GB ( /pub/pdb )
ftp_data       	Data directory within PDB ftp archive Approximately 129 GB ( /pub/pdb/data )
ftp_derived    	Derived data directory within PDB ftp archive Approximately 120 MB ( /pub/pdb/derived_data )
ftp_doc        	Doc directory within PDB ftp archive Approximately 319 MB ( /pub/pdb/doc )
emdb		Top level of EMDB ftp tree approximately 47 GB ( /pub/emdb )

Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete --port=33444 \
rsync.wwpdb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF

Download coordinate files in PDBML Format (xml):

rsync -rlpt -v -z --delete --port=33444 \
rsync.wwpdb.org::ftp_data/structures/divided/XML/ ./XML

Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete --port=33444 \
rsync.wwpdb.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.wwpdb.org::emdb/structures/EMD-*/header/" ./header

Download directories/files for EMDB entry EMD-5001:

rsync -rlpt -v -z --delete --port=33444 \
rsync.wwpdb.org::emdb/structures/EMD-5001/ ./EMD-5001

Using ftp protocol:

ftp ftp.wwpdb.org

will connect to an anonymous ftp server containing the remediated wwPDB repository.

Download coordinate files in PDB Exchange Format (mmCIF):

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF

Download coordinate files in PDBML format:

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/XML

Download coordinate files in PDB format:

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb

Download EMDB data files:

ftp://ftp.wwpdb.org/pub/emdb/structures

Need further help with the US site: Please contact Wolfgang Bluhm (wbluhm@ucsd.edu) if you have any problems connecting to ftp.wwpdb.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/rcsb/pdb-remediated/data/structures/divided/mmCIF/ \
./mmCIF

Download coordinate files in PDBML Format (xml):

rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/XML/ \
./XML

Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/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

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):

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/mmCIF

Download coordinate files in PDBML format:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/XML

Download coordinate files in PDB format:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb

Download the full PDB ftp tree:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/

Download EMDB data files:

ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures

Need further help with the EBI site: Please contact Gaurav Sahni (gaurav@ebi.ac.uk) if you have any problems connecting to ftp.ebi.ac.uk.

PDBj:

Using rsync protocol:

rsync pdb.protein.osaka-u.ac.jp::

ftp            	Top level of PDB ftp tree approximately 130 GB ( /pub/pdb )
ftp_data       	Data directory within PDB ftp archive Approximately 129 GB ( /pub/pdb/data )
ftp_derived    	Derived data directory within PDB ftp archive Approximately 120 MB ( /pub/pdb/derived_data )
ftp_doc        	Doc directory within PDB ftp archive Aproximately 319 MB ( /pub/pdb/doc )
emdb		Top level of EMDB ftp tree Approximately 47 GB ( /pub/emdb )

Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/mmCIF/ ./mmCIF

Download coordinate files in PDBML Format (xml):

rsync -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/XML/ ./XML

Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/pdb/ ./pdb

Download EMDB map metadata header files (xml):

rsync -rlpt -v -z --delete --include "emd-*.xml" \
"pdb.protein.osaka-u.ac.jp::emdb/structures/EMD-*/header/" ./header

Download directories/files for EMDB entry EMD-5001:

rsync -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::emdb/structures/EMD-5001/ ./EMD-5001

Using ftp protocol:

ftp pdb.protein.osaka-u.ac.jp/

will connect to an anonymous ftp server at PDBj containing the remediated wwPDB repository.

Download coordinate files in PDB Exchange Format (mmCIF):

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/mmCIF/

Download coordinate files in PDBML format (all):

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/XML/

Download coordinate files in PDBML format (no-atom site information):

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/XML-noatom/

Download coordinate files in PDBML format (atom site information only):

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/XML-extatom/

Download coordinate files in PDB format:

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/pdb/

Download EMDB data files:

ftp://pdb.protein.osaka-u.ac.jp/pub/emdb/structures

Need further help with the PDBj site: Please contact PDBj http://www.pdbj.org/pdbj_contact.html if you have any problems connecting to pdb.protein.osaka-u.ac.jp