---
title: PDB Search outputs
description: Result interpretation and data formats for PDB structure search and download.
tags:
  - pdb
  - 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

| Field | Type | Description |
|-------|------|-------------|
| `total` | integer | Total number of matching structures in the PDB |
| `query` | string | The search query as sent to RCSB |
| `entries` | array | Enriched structure entries (up to 10 with full metadata) |
| `allPdbIds` | string[] | All matching PDB IDs (up to `limit`) |

### Structure entry fields

Each entry in the `entries` array contains:

| Field | Type | Description |
|-------|------|-------------|
| `pdbId` | string | 4-character PDB identifier |
| `title` | string | Structure title from the PDB deposition |
| `method` | string | Experimental method (X-RAY DIFFRACTION, ELECTRON MICROSCOPY, SOLUTION NMR, etc.) |
| `resolution` | number | Resolution in Angstroms (null for NMR structures) |
| `organism` | string | Source organism scientific name |
| `releaseDate` | string | Date the structure was released publicly |
| `rcsb_url` | string | Direct link to the structure on RCSB PDB |

### Example search output

```json
{
  "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

| Field | Type | Description |
|-------|------|-------------|
| `pdbId` | string | PDB identifier (uppercase) |
| `rcsb_url` | string | Direct link to the structure on RCSB PDB |
| `format` | string | File format ("pdb" or "cif") |
| `content` | string | Full structure file content as text |
| `size` | integer | File content length in characters |

### 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

| Metric | Meaning |
|--------|---------|
| Resolution <2.0 A | High quality, excellent for docking and detailed analysis |
| Resolution 2.0-3.0 A | Acceptable for most computational work |
| Resolution >3.0 A | Low quality, use with caution for detailed modeling |
| X-RAY DIFFRACTION | Most common method, resolution is reliable quality indicator |
| ELECTRON MICROSCOPY | Cryo-EM, good for large complexes, resolution improving rapidly |
| SOLUTION NMR | No resolution metric, provides ensemble of conformations |
| Multiple chains | May indicate biological assembly (homo/hetero-oligomer) |
| Ligands present | Co-crystallized ligand provides binding site information |

## Experimental method comparison

| Method | Typical resolution | Strengths | Limitations |
|--------|-------------------|-----------|-------------|
| X-ray crystallography | 1.0-3.5 A | Highest resolution, most structures | Requires crystals, static snapshots |
| Cryo-EM | 2.0-5.0 A | No crystals needed, large complexes | Lower resolution (improving), radiation damage |
| NMR | N/A (ensemble) | Solution state, dynamics | Size limit (~40 kDa), no resolution metric |
| Neutron diffraction | 1.5-2.5 A | Hydrogen positions visible | Very rare, requires large crystals |

## 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

| Field | Type | Description |
|-------|------|-------------|
| `error` | string | Error message describing the failure |

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

## Read next