Current Structure Myoglobin (1MBN) Sperm whale oxygen-storage protein, with heme cofactor

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Biochemistry Visual Atlas

Interactive exploration of protein structure, chemistry, evolution, and function.

Current Structure Myoglobin (1MBN)

Biochemistry Visual Atlas

An interactive learning environment for exploring protein structure, chemistry, evolution, and function.

Protein Explorer — Visualize and analyze experimentally determined protein structures.

Chemical Properties — Explore how pH, protonation, and charge influence biomolecular behavior.

Function & Prediction — Connect structure to biological function and compare experimental structures with predictive models (coming soon).

Protein Explorer

Chemical Properties

Function

Prediction

Atlas Overview

The atlas is organized into four modules: Protein Explorer for structure and conservation, Chemical Properties for pH and charge, Function for biochemical interpretation, and Prediction for future model-comparison tools.

Display

Palette

Protein

Show the atoms that participate directly when zooming into an interaction.

Structure View Controls

View Mode Keep Whole Structure View Auto-Zoom to Selected Residue

Use “Fit Whole Structure” when you need context. Use “Focus Selected Residue” when you need molecular detail.

Orientation

Cartoon helices show the protein fold. Ligands and cofactors are drawn as sticks and spheres when they are present in the loaded structure.

-amino-acid residues

8major alpha helices

pH & Charge

Use the Henderson-Hasselbalch relationship to connect pH, pKa, protonation state, and expected charge. These are typical teaching pKa values, not protein microenvironment calculations.

Ionizable group

7.0current pH

-pKa

-protonated

-deprotonated

-dominant form

-expected charge

Amino Acid Charge Explorer

Estimate the net charge of a free amino acid by summing the charge contribution from each ionizable group at the selected pH.

Amino acid

-approximate net charge

-charge category

-classification

-side chain

Ionizable group	pKa	Protonated	Deprotonated	Charge contribution

Buffer Explorer

Explore how buffer effectiveness depends on the relationship between pH and pKa.

Buffer pKa

7.0current pH

7.4buffer pKa

-[A-] / [HA]

-buffer range

-acid form HA

-conjugate base A-

Loaded Protein Example

Optional: inspect an ionizable residue from the loaded structure using the same pH value.

Protein residue

-fraction charged

Conservation

Choose a course protein, prepare a biologically related comparison set, compute conservation, map results onto the structure, and turn the pattern into structure-function reasoning.

Recommended Student Workflow

Select a learning classification and course protein.
Load the reference structure.
Review or customize comparison structures.
Compute conservation.
Map conservation to the structure.
Inspect conserved residues.
Generate and revise your CER response.

Learning classification

Course Protein

Reference Structure

Suggested Comparison Structures

Select related structures to prepare the comparison set.

Custom PDB ID

Selected Comparison Structures

Why compare related structures?

Related proteins often preserve important structural and functional features across evolution. Comparing biologically appropriate structures can help identify residues and regions that may be important for stability, ligand binding, catalysis, or biological function.

Conservation Readiness Summary

-reference structure

-selected comparison structures

-custom structures

-status

Conservation Results

CautionThis conservation analysis is designed for teaching and exploration. Results depend on comparison-structure choice, chain selection, sequence quality, and structural similarity. Interpret conservation as evidence, not absolute proof.

Not computed yetstatus

-reference PDB

0attempted

0successfully used

0skipped/failed

0warnings

Red: Highly conserved

Orange: Conserved

Yellow: Moderately variable

Blue: Variable

Gray: Unmapped or unavailable

What do the colors mean? Red/orange residues are more conserved. Blue residues are more variable. Gray residues could not be mapped or are unavailable.

Structure coloring limitationStructure coloring is mapped from conservation scores onto the reference PDB. Residue numbering and chain selection can affect interpretation, especially for structures with multiple chains, fragments, or engineered mutations.

Functional Features to Inspect

Interpret Your Conservation Map

Which residues or regions are most conserved?
Are conserved residues clustered near a ligand, cofactor, active site, or subunit interface?
What biochemical function might explain this conservation pattern?
Which regions are more variable?
Why might some surface residues tolerate more variation?
Choose one highly conserved residue. What might happen if it were mutated?

CER Scaffold Generator

Interpretation cautionConservation is evidence, not proof. A highly conserved residue may support function, folding, stability, or interaction with another molecule. A variable residue is not necessarily unimportant; it may tolerate substitution, occur on the surface, or vary among related species.

Layer

Show conserved residues in this layer only.

-fully conserved residues

-comparison structures

-residues in selected layer

-conserved in selected layer

Residue	Identity	Score	Category	Functional annotation	Student interpretation prompt