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Deposition Preparation Tools

Data Extraction

• pdb_extract: Extract and harvest data in PDBx/mmCIF format from structure determination programs
• SF-Tool: Convert structure factor files among various formats

Small Molecules

• Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands

Data Format Conversion

• PDBML2CIF: Convert PDBML-format data into PDBx/mmCIF-format
• PointSuite: Generate symmetry records for macromolecular assemblies with point and helical symmetries
• MAXIT: Translate data between file formats and more

Validation Services

Validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. These reports are developed using the recommendations of thewwPDB Validation Task Forces.

Reports for released entries are available from Structure Summary pages.

Validation reports for manuscript reviewers are created during annotation of deposited structures.

Information and example Validation Reports (at wwpdb.org).

Check your X-ray, NMR, or EM structures before depositing (standalone server).

Deposit 3D macromolecular structure data to the PDB

Have non-atomic coordinates, multi-scale structures obtained through integrative/hybrid (I/H) methods? Deposit at PDB-Dev which is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods.

Questions about your deposition?

Search by Unreleased & Access New Entries

The PDB archive is updated weekly in two phases

Phase I: Every Saturday by 3:00 UTC, for every new entry, wwPDB website provides sequence(s) (amino acid or nucleotide) for each distinct polymer and, where appropriate, the InChI string(s) for each distinct ligand and the crystallization pH value(s).

Phase II: Every Wednesday by 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.

As of Tue Sep 15 2020 there are 168889 structures.

Next data entry update in:

Search by Drugs & Drug Targets

Drugs & Drug Targets in the PDB have been mapped to DrugBank.

• 

  Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase

• 

  Drug: Atorvastatin (Lipitor)

3D Structure Viewers

View PDB structures in 3D using Mol* from any entry's Structure Summary page.

Pathway View

Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.

Maps can be accessed from the Protein View (see example P29401), and the main Pathway View page.

RCSB Protein Feature View

Provides a graphical summary of biological and structural protein features of PDB entities and how they correspond to UniProtKB  sequences. It loads features from RCSB PDB webservices and third party resources such as UniProtKB, CATH or SCOPe.

Learn more about RCSB Protein Feature View.

Examples: SARS-CoV-2 spike glycoprotein, H-Ras, and BRCA1

This feature is available in Structure Summary pages and Instance Sequence pages.

Human Gene View

Illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB structure protein chains (selected from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.

Learn more about Gene View.

Examples: Breast Cancer 1 (early onset) and Hemoglobin, Alpha 1 (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering an HGNC Human Gene Symbol below (examples).

Sequence & Structure Alignment

RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, TopMatch).

Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments and detection of circular permutations.

Protein Symmetry

The JSmol symmetry display mode (select the Symmetry button) highlights global, local, and helical symmetry among subunits. The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.

• Hemoglobin

  

  PDB ID:4HHB

• Streptavidin

  

  PDB ID:1STP

• Inovirus

  

  PDB ID:1IFD

Structure Quality

Structure Summary pages provide access to information about structure quality.

The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks (black vertical boxes) are calculated with respect to all X-ray structures available prior to 2011. Resolution-specific percentile ranks (white vertical boxes) are calculated considering entries with similar resolution.

This graphic is from the wwPDB Validation Report , which provides a more detailed assessment of the quality of a structure and highlights specific concerns. These reports were created using the recommendations of wwPDB Validation Task Forces.The full wwPDB Validation Report PDF is available for download. PDFs of Ramachandran plots (created by MolProbity) are provided to offer an independent method to evaluate the conformational quality of protein structures.

For examples, view the Structure Summary pages for 1CBS (1.8Å structure of a small protein and a ligand , an entry with better overall quality relative to all X-ray structures) and 1FCC (a 3.2Å structure with worse overall quality relative to all X-ray structures).

Map Genomic Position to Protein

Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the location of a gene location (i.e., the site of a SNP).

Example of SNP in Breast Cancer 1 Gene

A TGT-to-GGT transversion in codon 64 of the BRCA1 gene leads to substitution of glycine for cysteine. This SNP is located on chromosome 17 at genomic coordinate: 43,106,478. The new mapping tool can be used to locate this position on the UniProt sequence and 3D structure.

EPPIC Biological Assemblies

EPPIC (Evolutionary Protein-Protein Interface Classifier) provides value-added information about biological assemblies in the PDB. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring.

Download Coordinate & Experimental Data Files

By entering PDB IDs, multiple files can be downloaded in batches containg one or more file formats.

Coordinate Data Files can be downloaded in the following formats:

• PDB
• PDBx/mmCIF
• PDBML/XML
• PDBML/XML (Header only)
• Biological Assemblies in PDB
• Biological Assemblies in PDBx/mmCIF

Experimental Data Files can be downloaded in the following formats:

• Structure Factors
• NMR Restraints
• Chemical Shifts
• NMR Restraints v2

Go to the Downloads Page

Download: Sequences

By entering PDB IDs, sequences can be downloaded in FASTA format.

Sequences can be provided for any of these identifiers:

• Entry IDs
• Entity IDs
• Asym IDs

Go to the Sequences Downloads Page

By entering chemical component IDs, SDF files with ligand coordinates can be downloaded.

Downloads are provided for:

• Coordinates of first chemical component instance from each PDB entry
• Coordinates of all chemical component instances from each PDB entry
• Ideal coordinates from Chemical Component Dictionary

Go to the Ligands Downloads Page

FTP Services

Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the wwPDB at at FTP archive, ftp.wwpdb.org (data download details) and Versioned FTP, ftp-versioned.wwpdb.org (Versioning details).

Major Directories

• The directory pub/pdb is the entry directory for the ftp site.
• The directory pub/pdb/data/structures/divided contains the current PDB contents including PDB, mmCIF, and PDBML/XML formatted coordinate files, structure factors and NMR restraints

Annual snapshots of PDB Archive are available. 

The Versioned FTP Archive is available at ftp://ftp-versioned.wwpdb.org (See announcement). 

HTTP/HTTPS Services

PDB structure files, chemical component files, and several other files are available for download via http/https. These URLs are useful in scripted downloads using utilities such as wget.

Downloadable Files

• PDB Structure Files
• Ligand Files
• Secondary Structure Files
• SIFTS Files

Web Services

Programmatic access to individual structures and/or specific data items is provided through Web Service Application Program Interfaces (APIs).

New Web Service APIs are being developed; users should register with the RCSB PDB API electronic list for announcements.

Contact RCSB PDB with questions suggestions for specific services.

Molecular explorations
through biology and medicine

PDB-101 is an online portal for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids.

Browse all PDB-101 resources by biological theme or start exploring: