Archive of experimentally determined 3D structures of biological macromolecules. Established in 1971, by Research Collaboratory for Structural Bioinformatics (RCSB), Brookhaven National Laboratories, USA. Archive contain atomic coordinates, bibliographic citations, primary and secondary structure information, crystallographic structure factors, NMR experimental data.

1. Protein Data Bank
(PDB)
Amandeep Singh
Assistant Professor
Department of Biotechnology
GSSDGS Khalsa College Patiala

2. Introduction
Experiments
3D structure of
biological
macromolecules
Archive
• Archive of experimentally determined 3D structures of biological macromolecules.
• Established in 1971, by Research Collaboratory for Structural Bioinformatics (RCSB),
Brookhaven National Laboratories, USA.
• Archive contain atomic coordinates, bibliographic citations, primary and secondary
structure information, crystallographic structure factors, NMR experimental data.

3. 43,186 Structures (1 May, 2207)
162269 Structures (1 April 2020)
PDB
Archive
X-Ray
Diffraction
NMR
Neutron
diffraction
Cryo electron
Microscopy
Secondary Data
Source of
Primary Data
Released data
Un-released data

4. Harnessing data from PDB
X-Ray
Diffraction
NMR
Neutron
diffraction
Cryo electron
Microscopy
Structure
File
mmCIF
format
PDB
format
PDBML/XML
format
3 Formats
Uncompressed
File
Compressed/Zip
File
(To reduce size)

5. Data Deposition Tools
1. Auto Dep Input Tool (ADIT)
Helps in depositing structures to PDB.
Structure Validation Database
Submission
Structural
Coordinate
Structure
Factor File

6. Structure factor and Coordinate
Electron
distribution
Coordinates of
each atom
Dots
Intensity of
X-Ray
Phase of
X-Ray
Structure factor Electron Density Map

7. Data Deposition Tools
2. pdb_extract
X-Ray
Diffraction
NMR
Neutron
diffraction
Cryo electron
Microscopy
Structure
File
Statistical
Information
Assemble
To reduce
Manual labor

8. pdb_extract Files
pdb_extract
2 mmCIF Files
macromolecular Crystallographic Information File
File 1 File 2
Structural Factors Atomic Coordinates
Structure determination statistics
Serve as Input for PDB deposition

9. Data Deposition Tools
3. Ligand deposit
Provide information about small molecules (ligands) bound to macromolecules
Small
molecules Large molecule
Chemical
Information
Structural
Information

10. Data Deposition Tools
4. Validation server
Provide opportunity for checking format of coordinate file and Structure factor file.
Structure Validation Database
Submission
Structural
Coordinate
Structure
Factor File

11. Validation
Structural
Coordinate
Structure
Factor File
PDB or mmCIF mmCIF or PDBML/XML
Yes No
Submitted
Changes
Submitted
Yes No
Submitted
Changes
Submitted
Pre-Check
Validation

12. 4. Validation server
• It also check entries which should have Unit cell, space groups, chain IDs, TER
card (at the end of each chain)
• Time taken for validation depends upon the size of the structure.
Final report
Summary reportAtlas Entry Structural Information
• Bond distance
• Angle comparison
• Torsion angle comparison
• Base morphology
• Molecular graphic images