3D Macromolecular PDB Viewer
WebGL protein structure visualisation with secondary structure ribbons, AlphaFold pLDDT colouring and residue inspection.
How it works
PDB coordinates are rendered in WebGL, with residues coloured as helix or sheet from the file's own HELIX and SHEET records — there is no geometric (DSSP-style) assignment, so a file without those records, including every AlphaFold model, is drawn as coil. AlphaFold models can instead be coloured by pLDDT, the per-residue confidence score, which distinguishes well-predicted cores from regions the model is uncertain about. Alternate conformers beyond the first are not drawn.
Frequently asked questions
What does the pLDDT score in an AlphaFold model mean?
pLDDT is a per-residue confidence estimate from 0 to 100. Above 90 indicates high accuracy including side-chain placement; 70–90 indicates a well-modelled backbone; 50–70 should be treated with caution; below 50 usually signals an intrinsically disordered region rather than a poorly modelled one. Low-confidence stretches are often biologically meaningful — they frequently mark genuinely flexible loops.
How do I view a protein structure from the PDB?
Fetch the structure by its four-character PDB identifier, then choose a representation: ribbons show secondary structure and overall fold, surface representation shows binding pockets and shape complementarity, and stick or ball-and-stick shows atomic detail at an active site. Colouring by chain separates subunits; colouring by B-factor or pLDDT shows which regions are least certain.