fetch_pdb: Fetch structure information from RCSB

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Fetch structure information from RCSB

Description

Fetches structure metadata from RCSB. If you want to retrieve atom data such as positions, use the function fetch_pdb_structure().

Usage

fetch_pdb(pdb_ids, batchsize = 100, show_progress = TRUE)

Arguments

pdb_ids	a character vector of PDB identifiers.
batchsize	a numeric value that specifies the number of structures to be processed in a single query. Default is 100.
show_progress	a logical value that indicates if a progress bar will be shown. Default is TRUE.

Value

A data frame that contains structure metadata for the PDB IDs provided. The data frame contains some columns that might not be self explanatory.

• auth_asym_id: Chain identifier provided by the author of the structure in order to match the identification used in the publication that describes the structure.

• label_asym_id: Chain identifier following the standardised convention for mmCIF files.

• entity_beg_seq_id, ref_beg_seq_id, length, pdb_sequence: entity_beg_seq_id is a position in the structure sequence (pdb_sequence) that matches the position given in ref_beg_seq_id, which is a position within the protein sequence (not included in the data frame). length identifies the stretch of sequence for which positions match accordingly between structure and protein sequence. entity_beg_seq_id is a residue ID based on the standardised convention for mmCIF files.

• auth_seq_id: Residue identifier provided by the author of the structure in order to match the identification used in the publication that describes the structure. This character vector has the same length as the pdb_sequence and each position is the identifier for the matching amino acid position in pdb_sequence. The contained values are not necessarily numbers and the values do not have to be positive.

• modified_monomer: Is composed of first the composition ID of the modification, followed by the label_seq_id position. In parenthesis are the parent monomer identifiers as they appear in the sequence.

• ligand_*: Any column starting with the ligand_* prefix contains information about the position, identity and donors for ligand binding sites. If there are multiple entities of ligands they are separated by "|". Specific donor level information is separated by ";".

• secondar_structure: Contains information about helix and sheet secondary structure elements. Individual regions are separated by ";".

• unmodeled_structure: Contains information about unmodeled or partially modeled regions in the model. Individual regions are separated by ";".

• auth_seq_id_original: In some cases the sequence positions do not match the number of residues in the sequence either because positions are missing or duplicated. This always coincides with modified residues, however does not always occur when there is a modified residue in the sequence. This column contains the original auth_seq_id information that does not have these positions corrected.

Examples

pdb <- fetch_pdb(pdb_ids = c("6HG1", "1E9I", "6D3Q", "4JHW"))

head(pdb)

protti documentation built on Oct. 22, 2024, 1:06 a.m.