MOLECULAR BIOLOGY · 3D · THEORY

Life, atom by atom.

An interactive atlas connecting molecular geometry, energy, and biological information.

LOCAL LAB

Open a PDB structure

Local PDB file

AlphaFold DB provides AI-predicted models with a confidence score; they are not experimental structures, and this viewer does not run a new AlphaFold calculation. AlphaFold DB ↗

Try a validated structure

Load a PDB file or enter a four-character RCSB ID.

Atom coordinates come from the PDB file. Displayed bonds use CONECT records when available; otherwise they are inferred for visualization only.

PDB · ROTATE · ZOOMNo structure

CONSPFe

PAIR ANALYSIS · 3D OVERLAY

Compare two PDB structures

Load two RCSB IDs or PDB files. The viewer creates a centered overlay and a compatibility report that is transparent about its limits.

Structure A Structure B

or file Aor file B

Both files came from the same complex / 3D coordinate frame

Waiting for two structures.

Overlay—

Structure A—

Structure B—

Contacts / binding—

Chemical reaction—

A centered overlay is for visual shape comparison, not structural alignment. Contact statistics are calculated only when the structures already share a coordinate frame, for example after extraction from a co-crystallized complex. * Mass is an estimate based on modeled atoms. No result confirms binding or a reaction.

Energy

ATP stores chemical potential: phosphate hydrolysis shifts the balance of cellular reactions.

Information

Base pairs are more than shapes: their complementarity turns molecular geometry into reliable copying.

Coordination

In heme, an iron ion coordinates ligands and enables reversible oxygen transport.

RCSB PDB · PDB-101

Real structures to explore

Load the PDB IDs in the viewer above, or open the official entries for their coordinates, metadata, and validation.

MOTM 41HemoglobinPDB-101 article · oxygen transport→ PDB-101 PDB 4HHBDeoxyhemoglobinX-ray structure · 1.74 Å→ RCSB PDB MOTM 72ATP synthaseRotary molecular motor→ PDB-101 MOTM 23DNADouble helix and genomic information→ PDB-101 PDB 1BNAB-DNADNA dodecamer · 1.90 Å→ RCSB PDB

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