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A Structural View of Biology

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

Use this website to access curated and integrated biological macromolecular information in the context of function, biological processes, evolution, pathways, and disease states.


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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

Explore the PDB Archive

3D Structure: Jmol

The Jmol molecular viewer offers several options for display and analysis. Launch the viewer using the 3D View feature from any entry's Structure Summary or by entering an ID below. Learn more about Jmol.

  • Hemoglobin
    Jmol Thumbnail for Hemoglobin 4HHB

    PDB ID: 4HHB

  • Streptavidin
    Jmol Thumbnail for Streptavidin 1STP

    PDB ID: 1STP

  • Purine Nucleoside Phosphorylase
    Jmol Thumbnail for Purine Nucleoside Phosphorylase 4EAR

    PDB ID: 4EAR

Sequence & Structure Alignment

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

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Download: Structures

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Molecule of the Month

Articles describe the structure and function of a molecule, offer interactive views and discussion topics, and links to specialized pages to help explore specific example structures.

Select an article
AAA+ Proteases
ABO Blood Type Glycosyltransferases
Acetylcholine Receptor
Acetylcholinesterase
Aconitase and Iron Regulatory Protein 1
Actin
Actinomycin
Adenovirus
Adrenergic Receptors
Alcohol Dehydrogenase
Alpha-amylase
Aminoacyl-tRNA Synthetases
Aminoglycoside Antibiotics
Amyloid-beta Precursor Protein
Amyloids
Anabolic Steroids
Anthrax Toxin
Antibodies
Antifreeze Proteins
Apoptosomes
Aquaporin
ATP Synthase
Auxin and TIR1 Ubiquitin Ligase
Bacteriophage phiX174
Bacteriorhodopsin
beta-Secretase
Broadly Neutralizing Antibodies
Cadherin
Calcium Pump
Calmodulin
cAMP-dependent Protein Kinase (PKA)
Carbonic Anhydrase
Carotenoid Oxygenase
Cascade and CRISPR
Caspases
Catabolite Activator Protein
Catalase
Chaperones
Cholera Toxin
Circadian Clock Proteins
Citrate Synthase
Citric Acid Cycle
Clathrin
Collagen
Complex I
Concanavalin A and Circular Permutation
Crystallins
Cyclooxygenase
Cytochrome bc1
Cytochrome c
Cytochrome c Oxidase
Cytochrome p450
Dengue Virus
Dermcidin
Designed DNA Crystal
Designed Protein Cages
Designer Proteins
Dihydrofolate Reductase
DNA
DNA Helicase
DNA Ligase
DNA Methyltransferases
DNA Polymerase
Dynein
Ebola Virus Proteins
Elongation Factors
Enhanceosome
Epidermal Growth Factor
Erythrocruorin
Estrogen Receptor
Exosomes
Fatty Acid Synthase
Ferritin and Transferrin
Fibrin
G Proteins
GFP-like Proteins
Glucagon
Glucansucrase
Glucose Oxidase
Glutamine Synthetase
Glycogen Phosphorylase
Glycolytic Enzymes
Green Fluorescent Protein (GFP)
Growth Hormone
Hemagglutinin
Hemoglobin
HIV Capsid
HIV Envelope Glycoprotein
HIV Reverse Transcriptase
HIV-1 Protease
Hsp90
Hydrogenase
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
Importins
Influenza Neuraminidase
Insulin
Insulin Receptor
Integrase
Integrin
Inteins
Interferons
Isocitrate Dehydrogenase
Kinesin
lac Repressor
Lactate Dehydrogenase
Leptin
Luciferase
Lysozyme
Major Histocompatibility Complex
Mechanosensitive Channels
Messenger RNA Capping
Methyl-coenzyme M Reductase
Microtubules
Multidrug Resistance Transporters
Myoglobin
Myosin
Nanobodies
Neurotransmitter Transporters
Neurotrophins
New Delhi Metallo-β-Lactamase
Nitric Oxide Synthase
Nitrogenase
Nucleosome
O-GlcNAc Transferase
Oct and Sox Transcription Factors
Oxidosqualene Cyclase
P-glycoprotein
p53 Tumor Suppressor
Parvoviruses
PDB Pioneers
Penicillin-binding Proteins
Pepsin
Phenylalanine Hydroxylase
Photosystem I
Photosystem II
Phototropin
Poliovirus and Rhinovirus
Poly(A) Polymerase
Potassium Channels
Prions
Proteasome
Proton-Gated Urea Channel
Pyruvate Dehydrogenase Complex
Ras Protein
RecA and Rad51
Receptor for Advanced Glycation End Products
Restriction Enzymes
Rhodopsin
Rhomboid Protease GlpG
Ribonuclease A
Ribosomal Subunits
Ribosome
Riboswitches
Ricin
RNA Polymerase
Rubisco
Selenocysteine Synthase
Self-splicing RNA
Serotonin Receptor
Serpins
Serum Albumin
Simian Virus 40
Sliding Clamps
Small Interfering RNA (siRNA)
SNARE Proteins
Sodium-Potassium Pump
Src Tyrosine Kinase
Sulfotransferases
Superoxide Dismutase
T-Cell Receptor
TAL Effectors
TATA-Binding Protein
Tetrahydrobiopterin Biosynthesis
Thrombin
Thymine Dimers
Tissue Factor
Titin
Tobacco Mosaic Virus
Toll-like Receptors
Topoisomerases
Transfer RNA
Transfer-Messenger RNA
Transposase
Trypsin
Ubiquitin
Vaults
Vitamin D Receptor
Xanthine Oxidoreductase
Zinc Fingers

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.

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 Tuesday Sep 01, 2015 at 5 PM PDT there are 111749 structures.

Next data entry update in:

Structural Biology Knowledgebase

Collection of Research Highlights

Collection of Research Highlights

The Structural Biology Knowledgebase (SBKB) is a free resource supported by the Protein Structure Initiative that gathers the latest protein structures, models, targets, and annotations from over 100 data sources. Research highlights by SBKB and the Nature Publishing Group provide insights into biology and medicine, spanning from basic molecular biology to infectious diseases and pathogenesis to drug discovery. Reviews of novel bench methods as well as improvements to tried-and-tested techniques also help researchers with their lab work. There are more than 450 articles to learn from in this collection.Read More

Molecule of the Month

Amyloids

Amyloids

Proteins have evolved to fold into a functional shape, or in cases where a flexible tether is needed, to remain consistently unfolded. In some cases, however, proteins aggregate to form unwanted structures, which can have dangerous consequences. The amyloid-beta precursor protein is a perfect example.... Read More

Quarterly News (see archive)

July 2015 Issue

Articles describe the RCSB PDB's leadership transition anniversary, new website features for query and visualization, and the protein modeling results at the National Science Olympiad. RCSB PDB remembers Edgar Meyer and John Wooley. The Education Corner highlights the results of our High School Video Challenge. » 7/21/15

Annual Reports

2014 Annual Report

Download the 2014 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

Annual Report Archive