From October 1993 release Protein Data Bank entries (PDB) have been included in the CSD. At present only bibliographic and sequence information is available, but in the future 3D coordinates will also be stored. All PDB entries have a refcode of the form 0ABC0n where 0ABC is the PDB ID code.
For further information refer to Oct. 1993 release notes, pp.10-25a.
To start-up QUEST3D to search only PDB database:
VMS/VAX: QUEST PROBNAME TT: CSD$TOP:PDB UNIX: quest probname -db $CSDHOME/csd/pdbTo start-up QUEST3D searches of PDB and master CSD database:
VMS/VAX: QUEST PROBNAME TT: CSD$TOP:PDB, CSD$MASTER UNIX: quest probname -db $CSDHOME/csd/pdb MasterThen enter terminal type and menu in the normal way (see Section 3.1).
COMP Name of the macromolecular structure and its source QUAL Contains a maximum of 7 information types - PDB ID code, date of deposition, classification of macromolecule, experimental technique (if any recorded in PDB), date at which this entry supersedes an existing entry, name(s) of data contributors, resolution of study AUTH Name(s) of authors for principal publication JRNL CODE VOLU Journal coden, volume, page and year of principal publication PAGE YEAR PDBS Contains for each chain - Chain identifier (if recorded in the PDB), number of residues in chain, residue sequence for each chain.This information, except PDBS field (see below) can be searched for by using the keyword tests:
*COMPOUND, *QUALIFIER, *AUTHOR, *SURNAME, *CODEN, *VOLUME, *PAGE, *YEAR in the TEXT and NUMERIC sub-menus, (see Section 3.2 Exs.6,7).
The main keywords available are:
PSEQ Defines a sequence of residues and is very similar to PSEQ in PEPTIDE-SEQ sub-menu (see Ex.10). Can specify if residue is terminal or non-terminal (% or -), and the residues can either be amino-acids (as defined in PEPTIDE-SEQ sub-menu) or modified amino-acids, nucleotides, carbohydrates and their groups (full list in Vol.3, Appendix 16). More than one PSEQ in a test is possible. PDEF Defines a new set of residues (equivalent to PDEF in PEPTIDE-SEQ sub-menu). NRES Specification of number of residues in a chain: NRES .LO. n or NRES n-m (where LO = logical operator, n<m). NCHAin Specification of number of chains in an entry: NCHA .LO. n or NCHA n-m. SAME Applies when there is more than one search sequence in a test and defines that both sequences must be in the same chain. EXHA Exhaustive search for sequence in an entry. FULL Gives full display of sequence information for hit entries, command is of the form: FULL CHAIN or FULL ALL. (FULL CHAIN displays only complete sequences for chains in which the search sequence is located.)The same keywords will be available in the future menu interface.
PSEQ -GLU-GLU-SER- <R>
END <R> to finish PDB definition.
A hit entry is 01BI02. Glu-Glu-Ser is highlighted in the PDBS record.