Protein Structure

Follow the same amino acids from sequence to helices, sheets and an experimental fold.

Experimental ubiquitin fold with coral helices, a cyan beta sheet, and grey connecting loops and C-terminal region.

Structural referencePDB 1UBQ

Sequence → secondary structure → fold

The same 76 residues, two ways to see them.

Inspect a structural feature

Representation

Turn the trace30°Colour by experimental B factor

Green highlights the selected feature. The outlined point is the selected residue.

Inspect residue I23

Cα B factor: 9.92 Å²

This deposited atomic displacement parameter can reflect disorder and modelling effects. It is not an AlphaFold confidence score.

Whole chain · 76 residues

A single chain forms one compact ubiquitin fold. The line connects the alpha-carbon atom of each successive residue; it omits side chains and other backbone atoms.

Sequence position · 1–76

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

The trace uses deposited coordinates and secondary-structure assignments. It does not simulate folding or infer what a mutation would do. The molecular view above shows the detailed structure; this trace makes sequence position easier to follow.

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Quick reference

One chain, several structural levels

Sequence records the order of amino acids. Local backbone arrangements form helices and sheets, while the full chain packs into a three-dimensional fold. A view of the sequence and a view of the fold describe the same molecule.

A small experimental example

Human ubiquitin in PDB 1UBQ has 76 residues, a main alpha helix, a short 3₁₀ helix and a mixed five-stranded beta sheet. The experiment highlights the deposited assignments so you can compare sequence positions with their arrangement in space.

Read evidence with its meaning

This is an X-ray structure refined at 1.80 Å resolution. Its B factors describe atomic displacement in that crystallographic model; they are not prediction-confidence percentages. The final four residues have greater disorder. A single structure also does not show every conformation available to a protein.

Check your understanding Optional

Two beta strands are far apart in sequence but adjacent in the structure. What does that show?

Their amino-acid sequence must have been rearranged.Folding brings separate regions of one chain together.They must belong to different proteins.

At the bench

Use Protein to inspect experimental structures, predicted models, sequence annotations and source evidence for proteins relevant to your work.

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Sources and model notes

Structure-based views of resolved experimental coordinates. Cutaways, category colours, camera choices and guided highlights are authored for teaching. Coordinates remain fixed; highlights are not experimental trajectories or simulation outputs.

RCSB PDB · Ubiquitin 1UBQ

Experimental coordinates, 76-residue sequence and primary structural publication. Feature ranges come from the deposited mmCIF assignments.

RCSB PDB-101 · Experimental methods

How experimental evidence supports structural models.