PDB Beta Archive

Introduction

wwPDB anticipates four character PDB accession code (PDB ID) will be consumed by 2028. With the continuous growth of PDB archive, wwPDB has revised PDB accession code by extending its length and prepending "PDB" (e.g., "1abc" will become "pdb_00001abc"). This new ID format will enable text mining detection of PDB entries in the published literature and allow for more informative and transparent delivery of revised data files.

PDB Beta Archive is provided to help community adopt extended PDB ID and PDBx/mmCIF format during the transition phase. All files at this archive are re-organized with extended PDB ID (including file naming and directories) at entry level, mirroring the same data organization of the PDB Versioned Archive.

All data files for a particular entry are stored in a single directory, labeled based on a two-character hash generated from the penultimate two characters of the PDB code, i.e., https://files-beta.org/pub/wwpdb/pdb/data/entries/<two-letter-hash>/<pdb_accession_code>/<entry_data_File_names>.

The two-letter hash will be based on the second and third characters from the last character. For example, PDB entry PDB_1abc5678 will be under /67/. This will maintain consistency with the current PDB archive: PDB entry 1abc is under /ab.

File naming is standardized such that the file type is used for the extension. For example, file naming is changed from r116dsf.ent.gz to pdb_0000116d-sf.cif.gz for the structure factor file and from pdb318d.ent.gz to pdb_0000318d.pdb.gz for the legacy PDB formatted coordinate file.

When four character PDB IDs are consumed, this PDB Beta Archive will replace the current PDB Archive and entries with extended PDB IDs issued are not compatible with PDB format. Please note that all existing legacy PDB format files will be frozen (will not be updated) at this PDB Beta archive, wwPDB encourages scientific journals, PDB community and users to transition to PDBx/mmCIF format and adopt new PDB ID format as earlier as possible.

For more information, see FAQ.

File Download

The PDB Beta archive is updated every Wednesday at 00:00 UTC.

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New Sequence and InChI

Every Saturday by 3:00 UTC, for every new entry the wwPDB website provides:

Sequence(s) (amino acid or nucleotide) for each distinct polymer (new_release_structure_sequence.tsv)
InChI string(s) for each distinct ligand (new_release_structure_nonpolymer.tsv), where appropriate
Crystallization pH value(s) (new_release_crystallization_pH.tsv)

Data Structure and Content

Primary data (atomic coordinates and experimental data) are stored at entry level using a hash directory.

Data types	File formats	Location
Atomic coordinates	PDBx/mmCIF, XML, and PDB	https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/ https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/[2-letter-hash]/[extended-PDB-ID]/structures/
X-ray data: Structure Factors	PDBx/mmCIF	https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/ https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/[2-letter-hash]/[extended-PDB-ID]/structures/
NMR data: Restraints and chemical shifts	NEF (/nmr_data), NMR-STAR, and native refinement program formats	https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/ https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/[2-letter-hash]/[extended-PDB-ID]/structures/
Small molecules references: CCD BIRD Other derived data: CCD holdings SMILES, InChI, InChIKey Variants	PDBx/mmCIF JSON SDF, smi, inch	https://files-beta.wwpdb.org/pub/wwpdb/refdata/ CCD: https://files-beta.wwpdb.org/pub/wwpdb/refdata/chem_comp/[last-character-hash]/[CCD ID]/ BIRD: https://files-beta.wwpdb.org/pub/wwpdb/refdata/bird Other derived data: https://files-beta.wwpdb.org/pub/wwpdb/refdata/derived_data/ CCD holdings: 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. https://files-beta.wwpdb.org/pub/wwpdb/refdata/derived_data/refdata_id_list.json.gz
Assemblies	PDBx/mmCIF	https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/ https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/[2-letter-hash]/[extended-PDB-ID]/assemblies/
Archive holdings	JSON	https://files-beta.wwpdb.org/pub/wwpdb/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).
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):

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Using rsync protocol:

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ftp_data        Data directory within PDB ftp archive ( /pub/wwpdb/pdb/data )
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Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete --port=33444 \
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[]
rsync -rlpt -v -z --delete --port=33444 \
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PDBe:

Using http protocol:

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Using rsync protocol:

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Download coordinate files in PDBML Format (xml):

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PDBj:

Using http protocol:

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Download coordinate files in PDBML format (all):

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

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

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Download the validation report files:

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Using rsync protocol:

rsync rsync-beta.pdbj.org::

ftp             Top level of PDB ftp tree ( /pub/wwpdb/pdb )
ftp_data        Data directory within PDB ftp archive ( /pub/wwpdb/pdb/data )
ftp_refdata     Small molecule data directory within PDB ftp archive ( /pub/wwpdb/refdata )
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Download coordinate files in PDBML Format (xml):

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Download chemical component (CCD) files:

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Using ftp protocol:

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Archive Snapshots

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HTTP Protocol

RCSB PDB (US/AWS): AWS S3 Explorer

PDBj (Japan): PDB Snapshot Archive

RSYNC Protocol

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

FTP Protocol

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

AWS SYNC Protocol

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

AWS SYNC Instruction:

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.
- Sync PDB Snapshots
- All PDB Snapshot objects
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- Specific PDB snapshot object (e.g., /20250101)
- aws s3 sync s3://pdbsnapshots/20250101/ ./local-directory/20250101 --no-sign-request