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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

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:

  1. Only recognized element symbols are used.
  2. Each element is followed by a count. A count of 1 may be omitted.
  3. A space or parenthesis must separate each count.
  4. 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.