PDB Search outputs

Search returns ranked structure metadata — PDB ID, title, resolution, method, and organism — while download returns the full structure file content. Use the metadata (resolution above all) to pick the best entry, then feed the downloaded structure straight into DiffDock, P2Rank, or PDB2PQR for your next step.

Output structure

PDB Search and PDB Download return different output formats. Search returns structured metadata, while Download returns structure file content.

PDB Search output

Top-level fields

Structure entry fields

Each entry in the entries array contains:

Example search output

{
  "total": 342,
  "query": "EGFR kinase",
  "entries": [
    {
      "pdbId": "1M17",
      "title": "Crystal structure of the EGFR kinase domain in complex with erlotinib",
      "method": "X-RAY DIFFRACTION",
      "resolution": 2.6,
      "organism": "Homo sapiens",
      "releaseDate": "2002-11-27",
      "rcsb_url": "https://www.rcsb.org/structure/1M17"
    },
    {
      "pdbId": "4HJO",
      "title": "Crystal structure of EGFR kinase domain with afatinib",
      "method": "X-RAY DIFFRACTION",
      "resolution": 2.05,
      "organism": "Homo sapiens",
      "releaseDate": "2012-10-24",
      "rcsb_url": "https://www.rcsb.org/structure/4HJO"
    }
  ],
  "allPdbIds": ["1M17", "4HJO", "3POZ", "2GS6", "5CNO", "7JXO"]
}

PDB Download output

Fields

PDB format content

The content field contains the complete PDB file, which includes:

• HEADER: Entry classification and deposition date
• TITLE: Structure title
• REMARK: Experimental details, resolution, refinement statistics
• ATOM/HETATM: Atomic coordinates for protein, ligands, and solvent
• CONECT: Bond connectivity for ligands and modified residues

mmCIF format content

When format: "cif" is requested, the content follows the mmCIF dictionary format with structured data categories:

• _entry: Entry identification
• _cell: Unit cell parameters
• _exptl: Experimental details
• _atom_site: Atomic coordinates (equivalent to ATOM/HETATM records)
• _struct: Structure description
• _refine: Refinement statistics

Canvas visualization

When PDB structures appear on the canvas:

• Border color: Green (#4CAF50)
• Tier 2 metrics: PDB ID, resolution, experimental method, chain count, ligand presence
• Tier 3: Interactive 3D Mol* viewer with the protein structure

Mol* viewer capabilities

• Rotate, zoom, and pan the 3D structure
• Color by chain, secondary structure, hydrophobicity, or B-factor
• Switch between cartoon, ball-and-stick, and surface representations
• Highlight specific residues or ligands
• Measure distances and angles

Interpreting canvas metrics

Experimental method comparison

Downstream data use

Chaining into DiffDock

Downloaded PDB structures serve as protein inputs for molecular docking. DiffDock also accepts a PDB ID directly, so you can skip the download step.

Chaining into P2Rank

The 3D structure is analyzed to predict ligand binding sites. P2Rank identifies surface pockets and scores them by predicted ligandability.

Chaining into PDB2PQR

The PDB structure is converted to PQR format with assigned protonation states and partial charges for electrostatic calculations.

Error responses

Common error values:

• "No structures found" — Search query matched zero entries
• "404 Not Found" — PDB ID does not exist (download)
• "RCSB API timeout" — Server did not respond in time; retry

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