Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox. Asymmetric Unit. Macromolecule Content Total Structure Weight: This is version 1. Crystal structure of uncleaved ovalbumin at 1. When you are performing a PCR or running a gel or constructing a recombinant vector, it is essential to know the DNA molecular weight of the samples.
This calculator could figure out the DNA molecular weight of one or multiple FASTA sequences simultaneously which are entered directly or uploaded with txt or fasta file extension. Note: Sequences are treated as sigle-stranded linear DNA with a 5' phosphate. No more than 3,, characters are recommended. Note: MW sense , MW anti-sense and MW both represents molecular weight of sense strand, anti-sense strand and double strand respectively.
RNA molecular weight is an important parameter for Molecular Biology. This calculator could figure out the RNA molecular weight of one or multiple FASTA sequences simultaneously which are entered directly or uploaded with txt or fasta file extension. Note: Sequences are treated as sigle-stranded linear RNA with a 5' triphosphate. Peptide or protein molecular weight is an important parameter for Molecular Biology. When you are isolating protein, purifying protein or analyzing concentration of protein, it is essential to know the peptide or protein molecular weight of the samples.
This calculator could figure out the peptide or protein molecular weight of one or multiple FASTA sequences simultaneously which are entered directly or uploaded with txt or fasta file extension. PNM in ball-and stick representation is covalently bound to Ser62 shown in stick representation. A special resource, the Biologically Interesting molecule Reference Dictionary BIRD , has been developed by the wwPDB to classify complex ligands that are composed of several subcomponents connected in a specific way.
These include peptide-like inhibitors and complex antibiotics, ribosomally synthesized gene products, such as thiostrepton found in PDB entry 1e9w , and products of nonribosomal enzymatic synthesis, such as vancomycin found in PDB entry 1sho.
BIRD is an external reference dictionary similar to the Chemical Component Dictionary that provides information about the chemistry, biology, and structure of complex ligands and peptide-like-molecules.
BIRD entries include molecular weight and formula, polymer sequence and connectivity, descriptions of structural features and functional classification, natural source if any , and external references to corresponding UniProt or Norine entries. The same BIRD molecule will have uniform representation across the archive. An important feature of BIRD is that both sequence and chemical information are provided, regardless of whether the molecule is represented as a polymer or as a ligand in the PDB archive.
BIRD is regularly reviewed for consistency and accuracy, and is used to uniformly annotate PDB entries containing these molecules. The dictionary is updated each week with new definitions as the corresponding PDB entries are released in the PDB archive. This feature is available for ligands with more than one atom ions excluded in PDB entries with structure factor data.
Different display thresholds sigma values can be selected default threshold is 1 sigma. This is useful for evaluating the experimental support for a particular ligand structure. For instance, in entry 1pwc , there is continuous electron density Figure 5 between C7 atom of the ligand and oxygen of serine 62 providing the evidence of covalent linkage between the protein and the ligand PNM which is open form of penicillin G.
Coordinates of the 'ideal' and 'model' versions of the ligand are available Figure 6. Ideal coordinates are calculated by software based on the known covalent geometry typically using the Molecular Networks Corina or OpenEye Omega programs.
PubMed uses cookies to keep a history of your searches. For you to use this feature, your Web browser must be set to accept cookies. Database records that you have copied to the Clipboard are represented by the search number 0, which may be used in Boolean search statements.
For example, to limit the records you have collected in the Clipboard to those from human, use the following search: 0 AND human[organism]. This does not change or replace the Clipboard contents. Search 5 : Use the search numbers shown in the "History section" of the advanced search page to combine previous searches for example, searches 2 and 3 shown above.
To do that, you can either: Click on the " Edit " link beneath the grey text box and type in a search statement such as: 2 AND 3 Or, instead of typing the search statement, use the " Add " link beside any search number in the " History " section of the Advanced Search page to add that search number into the grey text box. That will retrieve only records that contain human in the Organism field i. Compare the retrieval from this search with that of the sample basic search above.
Note that your search numbers might be different from those shown here, if you did earlier searches in the Entrez system before trying these examples.
Complex Boolean. Whether you are on the Basic search page i. Search Field names must be placed in square brackets [] , and can be written as either the full name, for example, [Database], or as the corresponding search field abbreviation, for example, [db] additional examples. Boolean operators are processed from left to right unless parentheses are used for nesting. Boolean operators can also be used to combine or subtract searches from each other i. To do this, use the Search History section of the Advanced Search page and simply enter the search numbers and desired Boolean operators in the query box.
For example, to identify the records that were retrieved by Search 2 of your search history, and also by Search 3, you could enter the following query: 2 AND 3 To identify the records that were retrieved by Search 2 but not by Search 3, you could enter the following query: 2 NOT 3. Search 6 : Simply enter all search terms and search fields as a single statement into the query box: human[Organism] AND p53 tumor suppressor[Title] Note that this search will produce the same results as sample searches 4 and 5, but it takes only a single step when entered directly into the search box as a Boolean query.
Search 7 : prostaglandin H2 synthase OR prostaglandin endoperoxide synthase NOT primates[Organism] OR rodents[Organism] This search will retrieve structure records that contain the terms prostaglandin H2 synthase OR prostaglandin endoperoxide synthase in any field, but that will not contain molecular components proteins, DNA, RNA from organisms in the taxonomic orders Primata or Rodentia. Range Search.
Range queries are constructed by specifying a lower and upper numerical value separated by a colon : to specify the range, followed by a search field name or abbreviation in square brackets, as shown in the examples to the right. You can insert a space on each side of the colon but that is not necessary; the search will work either way. All dates and all ' counts ' such as residue counts, molecule counts, etc. A specific example is provided in Search 10 to the right.
The search fields summary table includes the names and abbreviations for the various "date" fields. The search fields summary table includes the names and abbreviations for the various "counts" fields. Search 8 : Search 9 : 3 : 5[LigCount] This search of the Entrez Structure database will retrieve structures that have three to five different types of ligands bound chemicals in their biological unit.
A separate document describes how to find 3D protein structures bound to a specific chemical. Each protein sequence record will have a link to the corresonding structure record. Alternatively, you can select the " Find Related Data:Structure " option in the right margin of the search results page to retrieve the complete set of structure records that corresponds to the set of protein records you retrieved.
All Fields. Compare these search results with those obtained by the sample Citation Abstract Field search, which will retrieve structure records containing that phrase in the abstract of an associated PubMed record, and with those obtained by the sample Title field search, which will retrieve records containing that phrase only in the title of an associated PubMed record.
The quotes surrounding the search terms ensure they are searched as a phrase. The abstract if available of any PubMed reference linked to the structure. Compare these search results with those obtained by the sample All fields search, which will retrieve records containing that phrase in any field of the structure record, and with those obtained by the sample Title field search, which will retrieve records containing that phrase only in the structure title.
ASU Biopolymer Count. Compare with " BioUnit Biopolymer Count. In addition, the "Retrieve 3D Structures that have As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: 3[AsuBiopolymerCount] : 8[AsuBiopolymerCount] more about range searching The number of DNA molecules in the raw data for the structure i. ASU Chemical Count. The number of different types of chemicals not the total number of bound chemicals in the raw data for the structure i.
The bound chemicals are sometimes referred to as "ligands," hence the abbreviation [AsuLigCount]. Compare with " BioUnit Ligand Count. A separate file shows how to find 3D structures bound to a specific chemical e. The number of molecules in the raw data for the structure i. Examples include nucleotide or protein sequences that contain a large percentage of non-standard residues, long sugar chains e.
This field can be queried for a single value or a range of values. As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: 4[AsuOtherMoleculeCount] : 6[AsuOtherMoleculeCount] more about range searching The number of protein molecules in the raw data for the structure i.
As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: 4[AsuProteinMoleculeCount] : 6[AsuProteinMoleculeCount] more about range searching The number of RNA molecules in the raw data for the structure i. The name of any author associated with any PubMed reference linked to the structure. The format to search this field is: last name followed by a space and up to the first two initials followed by a space and a suffix abbreviation, if applicable, all without periods or a comma after the last name e.
Entrez automatically truncates on an author's name to account for varying initials, e. To turn off this automatic truncation, enclose the author's name in double quotes , e. Initials and suffixes may be omitted when searching, if desired. In that case, all authors with the specified last name will be retrieved, regardless of their initials. BioUnit Biopolymer Count. As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: 3[BiopolymerCount] : 8[BiopolymerCount] more about range searching The number of DNA molecules in the biological unit "biounit" of the structure.
BioUnit Chemical Count. The number of different types of bound chemicals not the total number of bound chemicals in the biological unit "biounit" of the structure.
The bound chemicals are sometimes referred to as "ligands," hence the abbreviation [LigCount]. BioUnit Molecular Weight. The molecular weight of the structure's biological unit "biounit" in KiloDaltons kDa. BioUnit Other Molecule Count. The number of molecules in the biological unit "biounit" of the structure that are not classified as a protein, DNA, RNA, or chemical , and therefore fall into the category of " other. As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: 4[OtherMoleculeCount] : 6[OtherMoleculeCount] more about range searching BioUnit Protein Molecule Count.
The number of protein molecules in the biological unit "biounit" of the structure. As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: 4[ProteinMoleculeCount] : 6[ProteinMoleculeCount] more about range searching The number of RNA molecules in the biological unit "biounit" of the structure. Chemical Name. The name of a ligand chemical that is present in a 3D structure record.
The same chemical might also be known by other names , which are indexed in the Chemical Synonyms search field. Use that field if you would like more comprehensive search results. A search of the "Chemical Name" field for "2-Hydroxybenzoic Acid" will therefore retrieve 1PTH along with other structures in which the authors used the same chemical name.
For broader search results , use the " Chemical Synonyms " field instead. That will allow you to enter any one of many names by which a chemical has been known.
For example, you could search for either "2-Hydroxybenzoic Acid" or "salicylate" or "2-Carboxyphenol" or another synonym and you will retrieve all macromolecular structures that contain salicylic acid , regardless of the chemical name that the authors used for it.
A separate file provides additional tips on how to find 3D structures bound to a specific chemical e. Tip: To search for other names by which the chemical has been known, such as "salicylate" or "2-Carboxyphenol," use the Chemical Synonyms search field.
The various names by which a given chemical structure has been known. For example, the terms "salicylate," "2-Hydroxybenzoic acid," "o-hydroxybenzoic acid," "2-Carboxyphenol," "o-Carboxyphenol," "2-hydroxy c benzoic acid," etc.
You can search the "Chemical Synonym" field for any of those terms in order to retrieve all of the 3D macromolecular structures that contain the chemical that is described in the corresponding PubChem Compound record CID The chemical names in this search field represent the filtered synonyms from PubChem Compound records that correspond to the chemicals present in the 3D macromolecular structure records. This search, for example, will retrieve 1PTH structure among others , even though the submitter of 1PTH used the term "2-Hydroxybenzoic Acid" instead of the term "salicylate" to refer to the chemical that is bound to Prostaglandin H2 Synthase.
Conserved Domain Database Description. See Conserved Domain Superfamily Description. Conserved Domain Description. Any term from the description of a conserved domain model. Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a specific hit to a conserved domain model whose description includes your query term.
A separate help document provides additional information about conserved domains. The position-specific scoring matrix PSSM identifier of a conserved domain that has been annotated as a specific hit on one or more protein molecules in a structure. Conserved Domain Short Name. The short name of a conserved domain. Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a specific hit to a conserved domain model bearing the short name of interest.
Conserved Domain Title. The title of a conserved domain. Note: A search of this field will retrieve 3D structures that contain at least one protein that has been annotated with a specific hit to a conserved domain model bearing the title of interest. Any term from the description of a conserved domain superfamily.
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily whose description includes your query term. The position-specific scoring matrix PSSM identifier of a conserved domain superfamily that has been annotated on one or more protein molecules in a structure. Conserved Domain Superfamily Short Name.
The short name of a conserved domain superfamily. Conserved Domain Superfamily Title. The title of a conserved domain superfamily. The name of an DNA molecule in a structure record. The DNA name often reflects the sequence of nucleotides in the molecule itself. The Enzyme Commission EC number of the PDB structure, representing the classification of an enzyme based on the chemical reactions it catalyzes. Note the queries 3. You can click on the Details folder tab of a search results page to see exactly how a query was handled by the Entrez system.
Experimental Method. The experimental method used to characterize the protein structure. Most structures are resolved using X-ray crystallography or nuclear magnetic resonance NMR but additional methods also exist e. To see the full list of experimental methods available, open the Advanced Search page, select the ExpMethod search field in the Search Builder section, and press the Show index link to browse the index of available terms. The description of the gene that codes for a protein molecule present in the structure record.
The gene description is the text that is present in the "summary" section of the corresponding Entrez Gene record. The association between the gene names and the protein molecules has been made using the method described under " Find related data.
The name of the gene that codes for a protein molecule present in the structure record. Because a gene may be known by a variety of names, this search field includes the official symbol and the alternative "also known as" gene symbols that are listed in the corresponding Entrez Gene record. The "Filter" search field allows you to narrow your retrieval to records that have certain attributes, such as record type e.
The "Filter" field also allows you to limit search results to structure records that have links to other Entrez databases of interest, as shown in the sample search to the right. A detailed explanation of each type of link is provided in the description of an Entrez search results page.
The Filter field can also be used to view current database statistics, by entering a search for All[Filt] , as shown in the example in the next column.
Conversely, it is possible to retrieve 3D structures that are bound to a specific chemical. Additional database statistics are available on the news page. The journal of the publication that reported the PDB structure findings. If more than one PubMed reference is associated with a structure record, the journal of each article has been indexed. Journal names can be written as full names or abbreviations. To see the list of journals, open the Advanced Search page, select the "Journal" search field in the Search Builder section, and press the Show index link to browse the index of available terms.
Science[jour] will retrieve structures published in the journal Science. This can represent the date on which a new Protein Data Bank structure record i.
It is an integer assigned consecutively to each structure record processed by NCBI. The latter is searchable in the PDB Accession field. The date on which the structure record was last modified. This was the case when the PDB database underwent a September remediation.
The following searches will retrieve updated structure records that were previously in MMDB but that have changed in some way, as well as new structure records that became available during the specified period of time: [MDAT] will retrieve the structure records that were updated and newly added to MMDB in the year A term representing the number of biopolymers i.
For example, this search field contains terms such as: monomeric dimeric trimeric tetrameric pentameric hexameric octomeric 9-meric meric Also note that the oligomeric state of a structure might reflect its bound state. A common name e. If a structure record contains protein or nucleotide sequences from more than one organism e. The summary page for an individual structure provides a list of the source organism s.
PDB Accession. It is generally a four-character alphanumeric combination e. PDB Chemical Code. The 3-letter code of a ligand bound chemical in the PDB structure. For example, HEM is the ligand code for a heme group in a globin. The classification of the PDB structure, as provided by the submitter in their data file. The more detailed description of the PDB structure. The earliest date that Protein Data Bank associates with an accession, generally representing the date on which the record was submitted to the PDB.
Note that the PDB Deposit Date is not necessarily the date on which the record became publicly available, and may be significantly different from the release date if submitters requested their data remain confidential until publication.
PDB Description. The number of PDB records that have been combined to reconstitute the originally submitted structure. Most structures occupy a single PDB record.
In other words, the search will retrieve all merged files from MMDB. This represents the term used by the author for the protein. The resolution in Angstroms of a protein structure resolved by diffraction or electron microscopy. As you can see by clicking on the Details folder tab after doing the search, each query above is translated to: The name of an RNA molecule in a structure record.
The RNA name often reflects the sequence of nucleotides in the molecule itself. The title of the publication s that reported the PDB structure findings. If more than one PubMed reference is associated with a structure record, the title of each article has been indexed.
Compare these search results with those obtained by the sample All Fields search, which will retrieve structure records containing that phrase anywhere in the record, and those obtained by the sample Citation Abstract Field search, which will retrieve structure records containing that phrase in the abstract of an associated PubMed record.
Additional note about links from Entrez Protein sequence records to structure records:. Protein sequence records can have a link to 3D structure record depending upon the data available for a particular protein sequence: Structure - Protein sequence records that have a direct association with the structure record because at least one of the following is true: a the protein sequence record was derived directly from a 3D structure record as described in MMDB data processing ; b the accession number of the protein sequence record was listed in the DBREF record of the PDB source file; c the protein accession listed in the DBREF record of the PDB source file is also found in an Entrez Gene record, and that Gene record also has links to other protein accession s ; in such a case, all of the protein accessions in the Entrez Gene record will have "Structure" links and will show a thumbnail image of a corresponding 3D structure in their protein sequence record display ; or d the protein is identical in composition and sequence length to any of the proteins noted in a , b , or c.
As of February , approximately 0. You can BLAST the protein sequence against the PDB structure database and adjust the algorithm parameters to decrease the stringency of the search, if desired. Summary -- a summary of all of the structure records default retrieved by your search, or for those you have selected with checkboxes, in HTML format. Note: The " Find Related Data " menu in the right margin of the search results page provides a complete list of links.
That menu retrieves related data for all records default retrieved by your search, or for the subset of records you have selected with checkboxes. Summary text -- a summary of the records retrieved by your search, in plain text format. By default, all records from your search result are listed. If you are interested only in specific records, select their checkboxes, select the desired display settings, and press "Apply" to view only those records.
The information shown for each record is the same as in the " Summary " format described above, but does not include the subset of links to additional information. UI List -- a list of the unique identifiers UI's for all of the structure records default retrieved by your search, or for those you have selected with checkboxes.
Items per page. By default, 20 documents are listed per page. If desired, decrease to a minimum of 5 or increase to a maximum of the number of documents displayed per page then press the "Apply" button. Sort by. Search results are displayed in order of decreasing relevance with respect to the query. Many search fields have a score or rank associated with them; for example, the Title and Organism fields have a high rank, while the PdbComment field has a lower rank.
The presence of a search term in any one or more of the fields is scored accordingly by the search system, and the total score given to a hit is used in determining its relevance to the query and therefore its placement on the search results page. Technical note : If you retrieve all records in the database by searching the Filter field for All[Filt] , the records are simply displayed in descending order of UID i.
Saves all the hits retrieved by your search into a plain text file, in either "Summary text " or "UI List" format.
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