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<!-- ============================================
::DATATOOL:: Generated from "mmdb1.asn"
::DATATOOL:: by application DATATOOL version 1.8.1
::DATATOOL:: on 01/18/2007 23:07:18
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "MMDB"
================================================= -->
<!--
$Revision: 6.1 $
**********************************************************************
Biological Macromolecule 3-D Structure Data Types for MMDB,
A Molecular Modeling Database
Definitions for a biomolecular assembly and the MMDB database
By Hitomi Ohkawa, Jim Ostell, Chris Hogue, and Steve Bryant
National Center for Biotechnology Information
National Institutes of Health
Bethesda, MD 20894 USA
July 1995
**********************************************************************
Contents of the MMDB database are currently based on files distributed by
the Protein Data Bank, PDB. These data are changed in form, as described
in this specification. To some extent they are also changed in content, in
that many data items implicit in PDB are made explicit, and others are
corrected or omitted as a consequence of validation checks. The semantics
of MMDB data items are indicated by comments within the specification below.
These comments explain in detail the manner in which data items from PDB
have been mapped into MMDB.
-->
<!-- Elements used by other modules:
Biostruc,
Biostruc-id,
Biostruc-set,
Biostruc-annot-set,
Biostruc-residue-graph-set -->
<!-- Elements referenced from other modules:
Biostruc-graph,
Biomol-descr,
Residue-graph FROM MMDB-Chemical-graph,
Biostruc-model FROM MMDB-Structural-model,
Biostruc-feature-set FROM MMDB-Features,
Pub FROM NCBI-Pub,
Date,
Object-id,
Dbtag FROM NCBI-General -->
<!-- ============================================ -->
<!--
A structure report or "biostruc" describes the components of a biomolecular
assembly in terms of their names and descriptions, and a chemical graph
giving atomic formula, connectivity and chirality. It also gives one or more
three-dimensional model structures, literally a mapping of the atoms,
residues and/or molecules of each component into a measured three-
dimensional space. Structure may also be described by named features, which
associate nodes in the chemical graph, or regions in space, with text or
numeric descriptors.
Note that a biostruc may also contain cross references to other databases,
including citations to relevant scientific literature. These cross
references use object types from other NCBI data specifications, which are
"imported" into MMDB, and not repeated in this specification.
-->
<!ELEMENT Biostruc (
Biostruc_id,
Biostruc_descr?,
Biostruc_chemical-graph,
Biostruc_features?,
Biostruc_model?)>
<!ELEMENT Biostruc_id (Biostruc-id*)>
<!ELEMENT Biostruc_descr (Biostruc-descr*)>
<!ELEMENT Biostruc_chemical-graph (Biostruc-graph)>
<!ELEMENT Biostruc_features (Biostruc-feature-set*)>
<!ELEMENT Biostruc_model (Biostruc-model*)>
<!--
A Biostruc-id is a collection identifiers for the molecular assembly.
Mmdb-id's are NCBI-assigned, and are intended to be unique and stable
identifiers. Other-id's are synonyms.
-->
<!ELEMENT Biostruc-id (
Biostruc-id_mmdb-id |
Biostruc-id_other-database |
Biostruc-id_local-id)>
<!ELEMENT Biostruc-id_mmdb-id (Mmdb-id)>
<!ELEMENT Biostruc-id_other-database (Dbtag)>
<!ELEMENT Biostruc-id_local-id (Object-id)>
<!ELEMENT Mmdb-id (%INTEGER;)>
<!--
The description of a biostruc refers to both the reported chemical and
spatial structure of a biomolecular assembly. PDB-derived descriptors
which refer specifically to the chemical components or spatial structure
are not provided here, but instead as descriptors of the biostruc-graph or
biostruc-model. For PDB-derived structures the biostruc name is the PDB
id-code. PDB-derived citations appear as publications within the biostruc
description, and include a data-submission citation derived from PDB AUTHOR
records. Citations are described using the NCBI Pub specification.
-->
<!ELEMENT Biostruc-descr (
Biostruc-descr_name |
Biostruc-descr_pdb-comment |
Biostruc-descr_other-comment |
Biostruc-descr_history |
Biostruc-descr_attribution)>
<!ELEMENT Biostruc-descr_name (#PCDATA)>
<!ELEMENT Biostruc-descr_pdb-comment (#PCDATA)>
<!ELEMENT Biostruc-descr_other-comment (#PCDATA)>
<!--
The history of a biostruc indicates it's origin and it's update history
within MMDB, the NCBI-maintained molecular structure database.
-->
<!ELEMENT Biostruc-descr_history (Biostruc-history)>
<!ELEMENT Biostruc-descr_attribution (Pub)>
<!--
The history of a biostruc indicates it's origin and it's update history
within MMDB, the NCBI-maintained molecular structure database.
-->
<!ELEMENT Biostruc-history (
Biostruc-history_replaces?,
Biostruc-history_replaced-by?,
Biostruc-history_data-source?)>
<!ELEMENT Biostruc-history_replaces (Biostruc-replace)>
<!ELEMENT Biostruc-history_replaced-by (Biostruc-replace)>
<!--
The origin of a biostruc is a reference to another database. PDB release
date and PDB-assigned id codes are recorded here, as are the PDB-assigned
entry date and replacement history.
-->
<!ELEMENT Biostruc-history_data-source (Biostruc-source)>
<!ELEMENT Biostruc-replace (
Biostruc-replace_id,
Biostruc-replace_date)>
<!--
A Biostruc-id is a collection identifiers for the molecular assembly.
Mmdb-id's are NCBI-assigned, and are intended to be unique and stable
identifiers. Other-id's are synonyms.
-->
<!ELEMENT Biostruc-replace_id (Biostruc-id)>
<!ELEMENT Biostruc-replace_date (Date)>
<!--
The origin of a biostruc is a reference to another database. PDB release
date and PDB-assigned id codes are recorded here, as are the PDB-assigned
entry date and replacement history.
-->
<!ELEMENT Biostruc-source (
Biostruc-source_name-of-database,
Biostruc-source_version-of-database?,
Biostruc-source_database-entry-id,
Biostruc-source_database-entry-date,
Biostruc-source_database-entry-history?)>
<!ELEMENT Biostruc-source_name-of-database (#PCDATA)>
<!ELEMENT Biostruc-source_version-of-database (
Biostruc-source_version-of-database_release-date |
Biostruc-source_version-of-database_release-code)>
<!ELEMENT Biostruc-source_version-of-database_release-date (Date)>
<!ELEMENT Biostruc-source_version-of-database_release-code (#PCDATA)>
<!--
A Biostruc-id is a collection identifiers for the molecular assembly.
Mmdb-id's are NCBI-assigned, and are intended to be unique and stable
identifiers. Other-id's are synonyms.
-->
<!ELEMENT Biostruc-source_database-entry-id (Biostruc-id)>
<!ELEMENT Biostruc-source_database-entry-date (Date)>
<!ELEMENT Biostruc-source_database-entry-history (Biostruc-source_database-entry-history_E*)>
<!ELEMENT Biostruc-source_database-entry-history_E (#PCDATA)>
<!--
A biostruc set is a means to collect ASN.1 data for many biostrucs in
one file, as convenient for application programs. The object type is not
inteded to imply similarity of the biostrucs grouped together.
-->
<!ELEMENT Biostruc-set (
Biostruc-set_id?,
Biostruc-set_descr?,
Biostruc-set_biostrucs)>
<!ELEMENT Biostruc-set_id (Biostruc-id*)>
<!ELEMENT Biostruc-set_descr (Biostruc-descr*)>
<!ELEMENT Biostruc-set_biostrucs (Biostruc*)>
<!--
A biostruc annotation set is a means to collect ASN.1 data for biostruc
features into one file. The object type is intended as a means to store
feature annotation of similar type, such as "core" definitions for a
threading program, or structure-structure alignments for a structure-
similarity browser.
-->
<!ELEMENT Biostruc-annot-set (
Biostruc-annot-set_id?,
Biostruc-annot-set_descr?,
Biostruc-annot-set_features)>
<!ELEMENT Biostruc-annot-set_id (Biostruc-id*)>
<!ELEMENT Biostruc-annot-set_descr (Biostruc-descr*)>
<!ELEMENT Biostruc-annot-set_features (Biostruc-feature-set*)>
<!--
A biostruc residue graph set is a collection of residue graphs. The object
type is intended as a means to record dictionaries containing the chemical
subgraphs of "standard" residue types, which are used as a means to
simplify discription of the covalent structure of a biomolecular assembly.
The standard residue graph dictionary supplied with the MMDB database
contains 20 standard L amino acids and 8 standard ribonucleotide groups.
These graphs are complete, including explicit hydrogen atoms and separate
instances for the terminal polypeptide and polynucleotide residues.
-->
<!ELEMENT Biostruc-residue-graph-set (
Biostruc-residue-graph-set_id?,
Biostruc-residue-graph-set_descr?,
Biostruc-residue-graph-set_residue-graphs)>
<!ELEMENT Biostruc-residue-graph-set_id (Biostruc-id*)>
<!ELEMENT Biostruc-residue-graph-set_descr (Biomol-descr*)>
<!ELEMENT Biostruc-residue-graph-set_residue-graphs (Residue-graph*)>
|
