Identifiers in PDB

Overview

Identifiers or IDs are commonly used in data resources to point to specific data contents. They may also be used to connect different data resources and indicate their relationships.

In the PDB, identifiers are used at all levels of the structural hierarchy in the entry. This includes:

  • 4-character PDB ID for the entry
  • Numeric ID for the assemblies in the entry
  • 1- or 2-character chain ID for instances of entities
  • 3-character IDs for residues and small molecules
  • “ATOM” or “HETATM” ID, and 4-character atom names for individual atoms

These identifiers are used to specifically select, visualize, locate a specific instance of a ligand, amino acid in a protein chain in a particular PDB entry. Hence learning about them can help specifically locate, visualize, and analyze all or specific parts of PDB structures.

Relevance of Identifiers in PDB Exploration

The PDB archives the location (three-dimensional coordinates) of each atom in a structure. In order to explore the structure and analyze molecular interactions in atomic detail, the locations of each atom in the PDB must be uniquely assigned. Various identifiers are used to specifically indicate one atom or groups of atoms. These identifiers enable users to visually or programmatically select one or more atoms of interest in order to visualize the selected atoms, specifically represent them as ribbons, ball and stick, or spacefill, and/or analyze them (such as measuring distances, angles, and torsions).

In addition, some IDs are also drawn from other data resources and are included either in the data files or in the RCSB archive for ease in connecting PDB data to related information (such as protein or nucleic acid sequences and EM maps). As a result, these IDs can be used for rapidly searching an archive for specific structures related to a topic of interest.

Identifiers, Conventions, and Examples

Various types of identifiers used at different levels of organization in the PDB are used for query and browsing. Some of the key identifiers used for searching, cross-referencing with other data resources, and pin-pointing data fields at various organizational levels are described here with examples. Learn more about Organization of 3D Structures in the Protein Data Bank.

Entry level Identifiers

Every structure in the PDB is assigned a 4-character alphanumeric identifier called the PDB identifier or PDB ID (e.g., 2hbs). In some cases, large groups of structures (e.g., a protein bound to a series of different inhibitors/drugs) are submitted to the PDB. In addition to PDB IDs these structures have an additional identifier, called the Group ID (e.g., G_1002018). The structure(s) may be described in the scientific literature, so associated PubMed IDs (e.g., 28436492) may be used to search the archive for these structures. Structures determined by Electron Microscopy must have associated EMDB IDs (e.g., EMD-21578) that connect the structure to EM maps that were used to solve the structure or to maps of related structures.

Entity level Identifiers:

Entities in the structure may be

  • macromolecules or polymers (e.g., proteins or nucleic acids)
  • oligosaccharides or branched polymers (e.g., hyaluronic acid)
  • small molecules or non-polymers (e.g., ligands, inhibitors, and individual residues)
  • complex small molecules with macromolecule-like composition (e.g., peptide-like inhibitors and antibiotics also called Biologically Interesting or BIRD molecules)

A Protein or peptide (short fragment of protein) whose sequence has been mapped to UniProt includes a UniProt Accession Code (e.g., P01019) for that entity. Similarly gene sequences mapped to GenBank have associated GenBank Accession Codes (e.g., 55771382).

A small molecule, ligand, or individual residue has a Chemical ID assigned in the Chemical Component reference Dictionary (e.g., ATP), while a complex small molecule such as a peptide-like inhibitor, antibiotic, or well-known di- or trisaccharide has a Biologically Interesting molecule Reference Dictionary identifier or BIRD ID (e.g., PRD_000006).

Within a PDB entry all entities are assigned unique IDs (e.g., entity 1). The Entity ID is specific to the particular structure (e.g., 4HHB_1 refers to entity 1 in PDB entry 4HHB) and is used to track its properties throughout the file - such as name, sequence, source, and links to IDs from other databases or dictionaries (e.g., UniProt, GenBank, Chemical, BIRD)

Instance level Identifiers:

An instance is a distinct copy of an entity or molecule. Instance level IDs are assigned according to the type of entity.

Macromolecular Instance ID

Macromolecules are polymeric chains made of covalently linked building blocks, such as amino acids and nucleotides. For each instance of protein or nucleic acid in the entry Chain IDs (e.g., A, A1, AA ) are assigned. Two sets of chain IDs are found in each PDB entry - one assigned by the PDB (label_asym_id), usually beginning with the alphabet A, and the other selected by the author (auth_asym_id) at the time of deposition. Most commonly both these chain IDs are the same but in some instances they may differ - e.g., in PDB ID 2or1, the author assigned chain IDs for the protein chains in the entry are L and R, while the PDB assigned ones are C and D respectively.

The polymer sequences are included in the PDB file, both in FASTA format (one-character codes) and as a list of Chemical IDs (or three-character codes) of amino acids from the N- to C-terminal end. Any residue in a polymer chain is specified by specifying its chemical ID (e.g., SER for the amino acid Serine) and residue number, or position in the polymer chain. Two residue numbering schemes are included for each residue (amino acid or nucleotide) in the file - a PDB assigned sequential numbering (label_seq_id) that starts from 1, and an author-specified numbering (auth_seq_id) that may match the numbering of related structures reported in the literature and/or the numbering of associated sequence database (e.g., UniProt) entries.

For example, in PDB ID 6kr6, the amino acids in protein Piwi have a PDB assigned sequential numbering from 1-810, while the author defined residue numbers are from 34-843 to match the UniProt numbering. While some visualization tools may display both residue numbers, as included in the cif format file, others tools may use only the one listed in the PDB format file, i.e., the residue numbers from the author.” Learn more about PDB and PDBx/mmCIF format files.

In some cases selected residues or parts of residues may have alternate locations as determined by the experiment. Each alternate location of a particular atom is differentiated with a unique Alt ID. For example, the residue number Ser 9 in Chain D in PDB entry 1trz has two atoms, each with alternate IDs A and B. When all the atoms of a structure have multiple locations, they are presented as multiple models and assigned unique Model IDs, often seen in NMR structures (e.g., PDB ID 2kpq).

Each atom in each residue is assigned a specific atom name in accordance with the Chemical Component Dictionary maintained by the PDB (e.g., N, CA, C, O, CB, OG are names of all the non-hydrogen atoms in Serine). All instances of serine in a structure will use the same atom names but will be assigned a unique combination of entity, and instance (or chain) ID, and residue number. If appropriate Alt IDs will also be specified. For example, in the PDB ID 1trz, chain ID D, Ser 9, two of its atoms (CB and OG) have Alt IDs A and B.

Small Molecule Instance ID

Small molecules such as ligands, ions, drugs, inhibitors, and individual residues (amino acids, nucleotides etc.) are found in PDB structures interacting with macromolecules such as proteins, and nucleic acids. They are assigned the chain ID of the (spatially) closest macromolecule. For example, all ligands, water molecules, etc. nearest protein chain A will also be assigned to chain A, though each of these small molecules will have unique residue numbers. So all ligands, waters etc. near a protein with chain ID A will be assigned the same chain ID. However, each of these small molecules and ligands can be specifically located by using unique residue numbers.

Atom names for all atoms in a small molecule are assigned according to the Chemical Component Dictionary.

Oligosaccharide Instance ID

Oligosaccharides are polymers of sugars that are covalently linked to form linear or branched chains. Like proteins or nucleic acids all instances of oligosaccharides are assigned unique chain IDs.

Oligosaccharides are often found covalently linked to protein (e.g., glycoproteins). If a single sugar molecule is covalently linked to a protein it is treated like a small molecule and assigned the chain ID of the protein it is linked to. If 2 or more sugars covalently linked to each other via glycosidic bonds they are assigned a unique chain ID.

Atoms in each sugar molecule are assigned atom names according to the Chemical Component Dictionary.

Assembly level Identifiers

Experimentally determined structures submitted to the PDB contain coordinates of macromolecules and small molecules that may represent a complete biologically relevant assembly, a portion of an assembly, or multiple copies of an assembly. Numerical Assembly IDs are assigned to each biologically relevant assembly. These IDs are entry-specific, can be used to visualize or download and provide instructions for defining specific biological assemblies. For example, when multiple assemblies are present in the entry (or structure), the assembly ID is used to group specific instances of entities that form each assembly (e.g., see PDB ID 2hbs). The Assembly ID may also be used for providing instructions to apply symmetry operations (denoted by Asymmetric Unit IDs for Asym IDs) to generate the biologically relevant assembly (e.g., see PDB ID 1out).



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Last updated: 2/24/2021