View PDB files in your browser
The Protein Data Bank's own format for proteins, DNA and the molecules bound to them. Open one right here in 3D. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your molecule opens in 3D, a protein's chains as a cartoon and a small molecule's atoms as balls and sticks, with its parts beside it and what you pick on the other side.
- Turn, zoom and move it • Double click to center on a point
- Cartoon, balls and sticks or spacefill • By element, chain or residue
- Inspect an atom • Its residue, chain, charge and B-factor
- Export • PNG, GLB, USDZ, STL and OBJ
About PDB
The Protein Data Bank has collected the shapes of proteins, DNA and RNA that scientists work out since 1971, and its PDB format, a line of 80 columns for each atom like the punched cards it began on, is how most of them were handed around for decades. The RCSB PDB, PDBe and PDBj serve entries as .pdb files, and the archive's own copies are named .ent.
Each line starts with what it holds: HEADER, TITLE and COMPND name the structure, SOURCE says where it came from, HELIX and SHEET give its folds, ATOM and HETATM every atom's name, residue, chain and place in Å, and CONECT the bonds of its ligands. A structure worked out by NMR keeps each of its models between MODEL and ENDMDL.
Filepeek reads it in your browser and draws the chains as a cartoon of their helices and sheets, with ligands and water as balls and sticks, or every atom as balls and sticks or spacefill, colored by element, chain or residue. Click an atom for its name, residue, chain and B-factor, measure between atoms, and Export saves the view as PNG or the model as GLB, USDZ, STL or OBJ.
Protein Data Bank file
.pdb • .ent
Format
- MIME type
- chemical/x-pdb
- Made by
- The Protein Data Bank, at Brookhaven National Laboratory
Inside the file
- Each line
- 80 columns, named by its first six
- Atoms
- Name, residue, chain and place in Å
- Also
- Title, source, helices, sheets and bonds
- Markup
- Plain text
Opens in every browser
Filepeek opens PDB files in 3D in Chrome, Edge, Firefox and Safari. On their own, browsers download them or show them as text.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open PDB
- WindowsNo app built in opens it • UCSF ChimeraX and PyMOL read it
- MacNo app built in opens it • UCSF ChimeraX and PyMOL read it
- iPhone and iPadNo app built in opens it • Save it here as USDZ to see it in your room
- AndroidNo app built in opens it • Save it here as GLB for 3D apps
Questions
Why are parts of my protein missing?
A crystal often leaves a protein's floppy loops and tails out of focus, so the file has no atoms for them and the chain shows a gap. Most X-ray structures leave out hydrogens too, as they're too small to see.
Why does my file show only one model?
A structure worked out by NMR keeps many models of the same molecule, one after another. Filepeek shows the first, and Show details says how many the file holds.
Why is there no PDB file for some structures?
PDB's columns fit at most 99,999 atoms and 62 chains, so since 2014 the biggest structures, like ribosomes, come as mmCIF instead. Filepeek opens those too.
What do the colors mean?
By element, carbon is gray, oxygen red, nitrogen blue, sulfur yellow and hydrogen white, as chemists have colored them since the CPK models. By chain, each chain has a color of its own, and by residue, each amino acid or base.
Is a .ent file the same as a .pdb?
Yes. The Protein Data Bank's archive names its PDB files like pdb1abc.ent, and Filepeek opens them like any PDB file.
Is every .pdb file a protein?
No. Visual Studio's program databases, which hold a program's debugging symbols, are .pdb files too, and so are some of Palm's old e-books. Filepeek tells them apart by what's inside: a PalmDOC book opens as a book, and a program database shows what it is.
Can I save it for 3D printing?
Yes. Choose Export, then Save as STL or OBJ for the style on show, or GLB for 3D apps and USDZ for an iPhone or iPad.