getpdb

Retrieve protein structure data from Protein Data Bank (PDB) database

Syntax

PDBStruct = getpdb(PDBid)

PDBStruct = getpdb(PDBid,Name=Value)

Description

PDBStruct = getpdb(PDBid) searches the PDB database for the protein structure record specified by the identifier PDBid and returns the MATLAB^® structure PDBStruct, which contains a field for each PDB record.

The Protein Data Bank (PDB) database is an archive of experimentally determined 3-D biological macromolecular structure data. getpdb retrieves protein structure data from the Protein Data Bank (PDB) database, which contains 3-D biological macromolecular structure data.

PDBStruct = getpdb(PDBid,Name=Value) specifies options using one or more name-value arguments in addition to the input argument, PDBid.

Examples

Retrieve Protein Structure Data from PDB Database

Retrieve the structure information for the electron transport (heme) protein that has a PDB identifier of 5CYT, read the information into a MATLAB® structure pdbstruct, and save the information to a PDB-formatted file electron_transport.pdb in the MATLAB® Current Folder.

pdbstruct = getpdb("5CYT",ToFile="electron_transport.pdb")

pdbstruct = struct with fields:
               Header: [1×1 struct]
                Title: 'REFINEMENT OF MYOGLOBIN AND CYTOCHROME C'
             Compound: [4×23 char]
               Source: [4×38 char]
             Keywords: 'ELECTRON TRANSPORT (HEME PROTEIN)'
       ExperimentData: 'X-RAY DIFFRACTION'
              Authors: 'T.TAKANO'
         RevisionDate: [1×7 struct]
           Superseded: [1×1 struct]
              Journal: [1×1 struct]
              Remark1: [1×1 struct]
              Remark2: [1×1 struct]
              Remark3: [1×1 struct]
              Remark4: [2×59 char]
            Remark100: [3×59 char]
            Remark200: [49×59 char]
            Remark280: [6×59 char]
            Remark290: [32×59 char]
            Remark300: [6×59 char]
            Remark350: [13×59 char]
            Remark500: [105×59 char]
            Remark525: [13×59 char]
            Remark620: [15×59 char]
            Remark800: [5×59 char]
         DBReferences: [1×1 struct]
    SequenceConflicts: [1×2 struct]
             Sequence: [1×1 struct]
            Heterogen: [1×2 struct]
        HeterogenName: [1×2 struct]
              Formula: [1×3 struct]
                Helix: [1×5 struct]
                 Link: [1×5 struct]
                 Site: [1×1 struct]
               Cryst1: [1×1 struct]
              OriginX: [1×3 struct]
                Scale: [1×3 struct]
                Model: [1×1 struct]
         Connectivity: [1×52 struct]
               Master: [1×1 struct]
            SearchURL: 'https://files.rcsb.org/download/5CYT.pdb'

Input Arguments

PDBid — Unique identifier for a protein structure record in the PDB database

string | character vector

Unique identifier for a protein structure record in the PDB database, specified as a string or character vector. Each structure in the PDB database is represented by a four-character alphanumeric identifier. For example, 4hhb is the identifier for hemoglobin.

Data Types: char | string

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: ToFile="electron_transport.pdb"

ToFile — File name or path and file name for saving PDB-formatted data

string | character vector

File name or a path and file name for saving the PDB-formatted data, specified as a string or character vector. If you specify only a file name, getpdb searches the MATLAB Current Folder.

Data Types: char | string

SequenceOnly — Control for returning the protein sequence only

false (default) | true

Control for returning the protein sequence only, specified as true or false .If there is one sequence, it is returned as a character array. If there are multiple sequences, they are returned as a cell array.

Data Types: logical

TimeOut — Connection timeout to retrieve data from the PDB database

5 (default) | positive number

Connection timeout to retrieve data from the PDB database, specified as a positive number. Specify the connection timeout value in seconds. For details, see here

Data Types: double

Output Arguments

PDBStruct — MATLAB structure containing a field for each PDB record

structure array

MATLAB structure containing a field for each PDB record, returned as a structure array. This table summarizes the possible PDB records and the corresponding fields in PDBStruct.

PDB Database Record	Field in the MATLAB Structure
HEADER	Header
OBSLTE	Obsolete
TITLE	Title
CAVEAT	Caveat
COMPND	Compound
SOURCE	Source
KEYWDS	Keywords
EXPDTA	ExperimentData
AUTHOR	Authors
REVDAT	RevisionDate
SPRSDE	Superseded
JRNL	Journal
REMARK 1	Remark1
REMARK N, where N equals 2 through 999.	Remarkn, where n equals 2 through 999.
DBREF	DBReferences
SEQADV	SequenceConflicts
SEQRES	Sequence
FTNOTE	Footnote
MODRES	ModifiedResidues
HET	Heterogen
HETNAM	HeterogenName
HETSYN	HeterogenSynonym
FORMUL	Formula
HELIX	Helix
SHEET	Sheet
TURN	Turn
SSBOND	SSBond
LINK	Link
HYDBND	HydrogenBond
SLTBRG	SaltBridge
CISPEP	CISPeptides
SITE	Site
CRYST1	Cryst1
ORIGXn	OriginX
SCALEn	Scale
MTRIXn	Matrix
TVECT	TranslationVector
MODEL	Model
ATOM	Atom
SIGATM	AtomSD
ANISOU	AnisotropicTemp
SIGUIJ	AnisotropicTempSD
TER	Terminal
HETATM	HeterogenAtom
CONECT	Connectivity

The Sequence field is also a structure containing sequence information in the following subfields:

• NumOfResidues

• ChainID

• ResidueNames — Contains the three-letter codes for the sequence residues.

• Sequence — Contains the single-letter codes for the sequence residues.

Note

If the sequence has modified residues, then the ResidueNames subfield might not correspond to the standard three-letter amino acid codes. In this case, the Sequence subfield will contain the modified residue code in the position corresponding to the modified residue. The modified residue code is provided in the ModifiedResidues field.

The Model field is also a structure or an array of structures containing coordinate information. If the MATLAB structure contains one model, the Model field is a structure containing coordinate information for that model. If the MATLAB structure contains multiple models, the Model field is an array of structures containing coordinate information for each model. The Model field contains the following subfields:

• Atom

• AtomSD

• AnisotropicTemp

• AnisotropicTempSD

• Terminal

• HeterogenAtom

The Atom field is also an array of structures containing the following subfields:

• AtomSerNo

• AtomName

• altLoc

• resName

• chainID

• resSeq

• iCode

• X

• Y

• Z

• occupancy

• tempFactor

• segID

• element

• charge

• AtomNameStruct — Contains three subfields: chemSymbol, remoteInd, and branch.

Version History

Introduced in R2006a