| PDB {SMRUCC.genomics.Data.RCSB.PDB} | .NET clr documentation |
The RCSB PDB file format is a standardized text-based format used to represent 3D structural data of biological macromolecules, such as proteins, nucleic acids, and viruses. Managed by the Research Collaboratory for Structural Bioinformatics (RCSB), it serves as the primary format for entries in the Protein Data Bank (PDB), a global repository for experimentally determined structures. Below is a detailed introduction:
Text-Based Structure: Plain text file (.pdb extension) with a fixed-column format, meaning data is organized into specific columns for consistency. Each line begins with a record type (e.g., ATOM, HETATM, HEADER) that defines the data it contains.
Core Components:
Atomic Coordinates: Stored in ATOM (standard residues) and HETATM (heteroatoms, e.g., water, ligands) records.
Metadata: Includes details like the title (TITLE), experimental method (EXPDTA), authors (AUTHOR), and biological source (SOURCE).
Sequence Information: Provided in SEQRES lines.
Secondary Structure: Annotated in HELIX, SHEET, and TURN records.
Connectivity: Bonds between atoms are listed in CONECT lines.
Crystallographic Data: Unit cell parameters (CRYST1), symmetry operations, and resolution.
Example ATOM/HETATM Line:
ATOM 2301 CA SER A 301 26.417 24.105 34.560 1.00 30.97 C
HETATM 9101 O HOH A 910 10.500 20.100 30.500 1.00 25.00 O Columns 1-6: Record type (e.g., ATOM).
Columns 7-11: Atom serial number.
Columns 13-16: Atom name (e.g., CA for alpha carbon).
Columns 17-20: Residue name (e.g., SER for serine).
Column 22: Chain identifier (e.g., A).
Columns 23-26: Residue number.
Columns 31-54: X, Y, Z coordinates.
Columns 55-60: Occupancy and temperature factor (B-factor).
Columns 77-78: Element symbol (e.g., C, O).
| Record | Description | |
|---|---|---|
HEADER | Molecular type, deposition date, and PDB ID (e.g., 1ABC). | |
TITLE | Title of the structure. | |
COMPND | Molecular components in the entry (e.g., protein, ligand, ion). | |
SEQRES | Amino acid/nucleotide sequence of the macromolecule. | |
ATOM | 3D coordinates of standard residues (e.g., amino acids in a protein). | |
HETATM | Coordinates of heteroatoms (non-standard residues: ligands, water, ions). | |
HELIX | Details of α-helices. | |
SHEET | Details of β-sheets. | |
CONECT | Bonds between atoms not covered by standard residue templates. | |
REMARK | Annotations, experimental details, or warnings. |
Column Width Restrictions: Legacy format limits data fields (e.g., residue numbers up to 9999, atom serial numbers up to 99,999).
Sparse Connectivity Data: Bonds are often inferred rather than explicitly listed.
No Support for Large Structures: Superseded by the mmCIF/PDBx format (more flexible, supports larger datasets).
The PDB now prioritizes the mmCIF format (Macromolecular Crystallographic Information File), which uses a flexible, key-value-based structure without column limits. Legacy PDB files are automatically converted to mmCIF for archiving.
Visualization: PyMOL, Chimera, VMD, RCSB PDB Viewer.
Analysis: BioPython, MDAnalysis.
Database Access: RCSB PDB website (search, download, and explore entries).
HEADER HYDROLASE 15-JUL-98 1ABC
TITLE CRYSTAL STRUCTURE OF EXAMPLE ENZYME
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: EXAMPLE ENZYME; CHAIN: A;
SEQRES 1 A 321 SER GLY LEU ARG TYR ...
ATOM 1 N SER A 1 10.000 20.000 30.000 1.00 25.00 N
ATOM 2 CA SER A 1 11.000 21.000 31.000 1.00 26.00 C
HETATM 1001 O HOH A 1001 40.000 50.000 60.000 1.00 30.00 O
HELIX 1 ALA A 10 THR A 20 1
CONECT 1001 1002Studying protein-ligand interactions.
Analyzing enzyme active sites.
Visualizing mutations in diseases.
Teaching structural biology concepts.
For more details, visit the RCSB PDB and explore entries like 1ATP.
pdb file is the struct data about a protein complex, one pdb file may includes multiple protein and metabolite compound data.
# namespace SMRUCC.genomics.Data.RCSB.PDB
export class PDB {
ANISOU: ANISOU;
# Populate out the multiple structure models inside current pdb data file
AtomStructures: iterates(Atom);
Author: Author;
CAVEAT: CAVEAT;
CISPEP: CISPEP;
Compound: Compound;
Conect: CONECT;
crystal1: CRYST1;
DbRef: DbReference;
Experiment: ExperimentData;
Formula: Formula;
Header: Header;
Helix: Helix;
Het: Het;
HetName: HetName;
HETSYN: HETSYN;
Journal: Journal;
Keywords: Keywords;
Links: Link;
Master: Master;
Matrix1: MTRIX123;
Matrix2: MTRIX123;
Matrix3: MTRIX123;
MaxSpace: Point3D;
MDLTYP: MDLTYP;
MinSpace: Point3D;
MODRES: MODRES;
# number of models inside current pdb file
NUMMDL: NUMMDL;
Origin1: ORIGX123;
Origin2: ORIGX123;
Origin3: ORIGX123;
Remark: Remark;
Revisions: Revision;
Scale1: SCALE123;
Scale2: SCALE123;
Scale3: SCALE123;
seqadv: SEQADV;
Sequence: Sequence;
Sheet: Sheet;
SIGATM: SIGATM;
SIGUIJ: SIGUIJ;
Site: Site;
Source: Source;
# the input data text of this pdb object
SourceText: string;
SPLIT: SPLIT;
SPRSDE: SPRSDE;
SSBOND: SSBOND;
Title: Title;
}
ANISOU: ANISOUAtomStructures: iterates(Atom)Author: AuthorCAVEAT: CAVEATCISPEP: CISPEPCompound: CompoundConect: CONECTcrystal1: CRYST1DbRef: DbReferenceExperiment: ExperimentDataFormula: FormulaHeader: HeaderHelix: HelixHet: HetHetName: HetNameHETSYN: HETSYNJournal: JournalKeywords: KeywordsLinks: LinkMaster: MasterMatrix1: MTRIX123Matrix2: MTRIX123Matrix3: MTRIX123MaxSpace: Point3DMDLTYP: MDLTYPMinSpace: Point3DMODRES: MODRESNUMMDL: NUMMDLOrigin1: ORIGX123Origin2: ORIGX123Origin3: ORIGX123Remark: RemarkRevisions: RevisionScale1: SCALE123Scale2: SCALE123Scale3: SCALE123seqadv: SEQADVSequence: SequenceSheet: SheetSIGATM: SIGATMSIGUIJ: SIGUIJSite: SiteSource: SourceSPLIT: SPLITSPRSDE: SPRSDESSBOND: SSBONDTitle: Title