Biology and Chemistry Report

Provides a detailed covalent, molecular and genetic description of a single structure entry. The report includes the following information:

• Structural Details

• Polymeric Molecules

• Entity Poly

• Ligand and Prosthetic Groups

• Natural and Genetic Source

• Additional Information

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Structural Details

This section includes the following item:

Field	Definition	Example	mmCIF token displayed	Relationship to the PDB File
Keywords	Category specific keywords that describe the chemical nature of the structure	RNA binding protein	struct_keywords.pdbx_keywords	Found in the KEYWDS record.
Text	Descriptive terms of the particular structure entry.	serine protease	struct_keywords.text	Found in the KEYWDS record

 

 

Polymeric Molecules

A descriptive summary of all the biological entities that compose a single structure and contains the following categories:

 

Field	Definition	Example	mmCIF token displayed	Relationship to the PDB File
Chain	Chain id for the entity.	RNA binding protein	pdbx_poly_seq_scheme.pdb_strand_id	Found in the COMPND record
Description	Descriptive terms of the particular structure entry.	Serine protease	entity.pdbx_description	Found in the COMPND record
Fragment	Describes a subset of residues from the total gene product that was used in determining the structure.	Klenow Fragment	entity.pdx_fragment	Found in the COMPND record
Mutation	Point mutations in the entity from the wild type sequence of its associated gene product.	Y31H" (the entity was mutated from a tyrosine to a histidine at position 31).	entity.pdx_mutation	Found in the COMPND record
Source Method	Method by which the entity was produced for structure determination.	nat	entity.src_method	Found in the COMPND record
Entity Name	Common name for entity	HIV-1 protease monomer	entity_name_com.name	Found in the COMPND record
Entity Name Sys	Scientific name of the entity	acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta	entity_name_sys.name	Found in the COMPND record

 

 

Additional names also include RCSB_NAME,RCSB_SYNONYM, SWS_NAME,SWS_KEYWORD, GB_NAME,GB_SYNONYM, GB-KEYWORD whereSWS is SwissProt and GB is Genbank.

 

Entity Poly

Summary of details about the polymer, such as the type of the polymer, the number of  monomers, and whether it has non-standard features. It contains the following categories:

 

Field	Definition	Example	mmCIF token displayed	Relationship to the PDB File
Entity	This data item is a pointer to entity.id in the ENTITY category.	1	entity_poly.entity_.id	Found in the COMPND record
Chirality	A flag to indicate whether or not the polymer contains at least one monomer unit with chirality different from that specified in entity_poly.type.	Enumerations of "no", "n", "yes", "y"	entity_poly.nstd_chirality	Found in the COMPND record
Linkage	A flag to indicate whether or not the polymer contains at least one monomer-to-monomer linkage different from that implied by entity_poly.type.	Enumerations of "no", "n", "yes", "y"	entity_poly.nstd_linkage	Found in the COMPND record
Monomer	A flag to indicate whether or not the polymer contains at least one monomer that is not considered standard.	Enumerations of "no", "n", "yes", "y"	entity_poly.nstd_monomer	Found in the COMPND record
# Mon	The number of monomers in the polymer.	None	entity_poly.number_of_monomers	Found in the COMPND record
Strand	The PDB strand/chain id(s) corresponding to this polymer entity.	A	entity_poly.pdbx_strand_id	Found in the COMPND record
Type	The type of the polymer.	polypeptide(L)	entity_poly.type	Found in the COMPND record
Details	A description of special aspects of the polymer type.	monomer Ala 16 is a D-amino acid	entity_poly.type_details	Found in the COMPND record

 

Ligand and Prosthetic Groups

A description of all chemical components including small molecules, metals and ions that are covalently or non-covalently bound to the structure, which includes the following categories:

 

Field	Definition	Example	mmCIF token displayed	Relationship to the PDB File
Name	Description of the component.	PROTOPORPHYRIN IX CONTAINING FE	entity.pdbx_description	Found in the COMPND record
Chemical Formula	Written according to the following rules: Only recognized element symbols are used. Each element is followed by a count. A count of 1 may be omitted. A space or parenthesis must separate each count. The ordering of element is according the "Hill" system of the Chemical Abstracts Service.	C34 H32 N4 O4 Fe	chem_comp.formula	Found in the FORMUL record
Weight	Formula Mass in Daltons	None	chem_comp.formula_weight	Found in the FORMUL record

 

Additional Field: Ligand Structure - clicking on the "View" launches the Ligand 2D applet.

 

Natural and Genetic Source

The organism in which the entity is found. (Note only the definitions of the common fields are shown).

 

 

Field	Definition	Example	mmCIF token displayed	Relationship to the PDB File
Common Name	Common name of the natural organism from which the gene was obtained.	yeast	entity_src_gen.gene_src_common_name entity_src_nat.common_name	Found in the SOURCE record
Scientific Name	Scientific name of the organism	Escherichia coli	entity_src_gen.pdbx_gene_src_scientific_name entity_src_nat.organism_scientific	Found in the SOURCE record
Gene	Identifies the gene		entity_src_gen.pdbx_gene_src_gene	Found in the SOURCE record
Host Common Name	The common name of the organism that served as host for the production of the entity	bacteria	entity_src_gen.host_org_common_name	Found in the SOURCE record
Host Scientific Name	The scientific name of the organism that served as host for the production of the entity.	Escherichia coli	entity_src_gen.host_org_scientific_name	Found in the SOURCE record
Host Strain	The strain of the organism in which the entity was expressed	AR120	entity_src_gen.pdbx_host_org_strain	Found in the SOURCE record
Host Vector Type	Identifies the type of vector (plasmid, virus, cosmid).	PLASMID	entity_src_gen.pdbx_host_org_vector_type	Found in the SOURCE record
Host Plasmid Name	The name of the plasmid that produced the entity in the host orgamism	pETC3C	entity_src_gen.plasmid_name	Found in the SOURCE record

 

 

Additional Information

 

EC Numbers - Provides direct links to the IUBMB Nomenclature Page, the KEGG Reference Pathways and the KEGG Pathways and Reactome links.

 

NCBI Entrez Gene - "Gene" provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites. The Entrez Gene page at NCBI can be accessed by simply clicking on the locus links IDs on the page

 

Online Mendelian Inheritance in Man (OMIM) - This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI.

 

Genome Information - Give details about the Chromosome, Loci, Gene Name and Symbol for the gene of a human protein. Also has links to "GeneCards", a database of human genes, their products and their involvement in diseases developed at the Weizmann Institute.

 

Single Nucleotide Polymorphisms (SNPs) - The Single Nucleotide Polymorphism database (dbSNP) is a public-domain archive for a broad collection of simple genetic polymorphisms provided by NCBI.