Online PDB Viewer: 3D Protein Structure Viewer

Open any PDB ID, a UniProt ID (AlphaFold model) or your own .pdb / .cif file and view the 3D structure in the browser: cartoon, surface and sticks, residue highlighting and pLDDT coloring. No install.

To view a PDB file online, type its 4-character PDB ID (for example 6M0J), a UniProt accession to load the AlphaFold model, or upload a .pdb or .cif file. The structure renders in 3D in your browser, where you can switch between cartoon, surface and stick views, highlight residues and color AlphaFold models by pLDDT confidence.

Free, runs in your browser. Nothing you enter is uploaded.

How to use it

Enter a 4-character PDB code or UniProt Accession ID (or upload a local .pdb/.cif file).
Select display representations: Cartoon, Surface, Sticks, or Ribbon.
Use the mutation highlight input to pinpoint variant residue locations in 3D.
Toggle pLDDT confidence coloring or Hydrophobicity heatmaps.

What you enter

Standard 4-letter RCSB Protein Data Bank accession code, UniProt ID, or local coordinate file (.pdb/.cif)
Optional residue position list for mutation highlighting (e.g. 484, 501)

What you get

Interactive 3D molecular visualization with Cartoon, Surface, Sticks, and Ribbon modes
Structural validation metrics (Resolution, R-factor, pLDDT distribution)
Distance measurement and mutation spatial neighborhood analysis

Formula

pLDDT = 100 * [ (1/N) * Σ Θ(|d_true - d_pred|) ]

Renders macromolecular atomic coordinates using 3Dmol.js WebGL graphics. AlphaFold confidence is graded by predicted Local Distance Difference Test (pLDDT): >90 (Very High), 70-90 (Confident backbone), 50-70 (Low/flexible), <50 (Disordered).

Example: SARS-CoV-2 Receptor Binding Domain (PDB: 6M0J)

Input: PDB ID: 6M0J | Focus Residues: K417, E484, N501 | Color by: Secondary Structure

Result: Renders ACE2-Spike complex with highlighted interfacial contact residues in stick representation.

Residues 484 and 501 locate directly at the ACE2 contact interface, demonstrating structural basis of variant affinity changes.

Questions

How do I open a PDB file online?

Upload the .pdb or .cif file, or type the 4-character PDB ID and the structure loads from the Protein Data Bank. Everything renders in your browser with WebGL; uploaded files are not sent to a server.

Can I view AlphaFold predicted structures?

Yes. Enter a UniProt accession (for example P0DTC2) to load the AlphaFold model, then color it by pLDDT to see which regions are predicted with high confidence (above 70) and which are likely disordered (below 50).

What is the difference between PDB and mmCIF files?

Both store atomic coordinates. The older PDB format has fixed-width columns and size limits; mmCIF (.cif) is the current standard used by the Protein Data Bank and handles very large structures. The viewer reads both.

What does pLDDT confidence mean in AlphaFold structures?

pLDDT (predicted Local Distance Difference Test) measures local structural confidence on a scale of 0 to 100. Scores above 70 indicate high confidence, while scores below 50 suggest disordered or flexible regions.

Limitations

Requires WebGL-enabled browser with hardware graphics acceleration for large structures (>50,000 atoms).
AlphaFold predicted structures represent static monomeric conformations and may not reflect multimeric assembly states or ligand-induced induced-fit rearrangements.

References

Jumper J et al. (2021) Nature 596(7873):583-589.
Rego N, Koes D (2015) Bioinformatics 31(8):1322-1324.

More Proteomics

All free tools · By Dr. Zubair Khalid, DVM, MS, PhD.