A Motif database with
structurally diverse loops and conserved frameworks
In the Protein Data Bank (PDB),
Loops are most variable regions in protein structures,
but their anchoring secondary structures are often conserved.
Therefore, there are many small motifs composed of variable loops and stable
alpha-helics or beta-strands.
This page provides some databases containing many such motifs derived from PDB.
See below example:
The picture is an example motif family in the database.
It clearly shows that loops have variable conformations and the
anchoring secondary structures are structurally conversed.
This family is composed of 6 motifs listed below:
| MOTIF ID |
SHEET |
LOOP |
SHEET |
| EE1bro-A_21_4 |
TSIDLYYEDH |
GTGQ |
PVVLI |
| EE1ede_42_7 |
AHYLDE |
GNSDAED |
VFLC |
| EE1ivy-A_40_10 |
KHLHYWFV |
ESQKDPENSP |
VVLWL |
| EE1tht-A_26_11 |
QELHVWET |
PPKENVPFKNN |
TILIA |
| EE1wht-A_36_10 |
RSLFYLLQ |
EAPEDAQPAP |
LVLWL |
| EE2ctc_53_8 |
PIYVLKF |
STGGSNRP |
AIWIDL |
Here, we define some terms used in this database.
Loop: defined by DSSP programs.
Motif: A alpha-helix [or beta-strand] -- loop -- alpha-helix
[or beta-strand] segment.
Framework: A pair of secondary structures (either alpha-helics
or beta-strands) bracing a loop.
Motif id: A unique id assigned to a motif such as EH1one-B_320_7,
here E and H are type of secondary structures,
1one is the PDB id, B is chain id in PDB,
320 is the residue number the loop begins, and 7 is the loop length.
This database is composed of main database and three sub-databases.
The main database
contains the motif families from all the PDB.
The first sub-database
comprises the motif families from homologous protein families.
In the second sub-database,
the loops in each motif family is of same length.
The the last sub-database
is the collection of loops with variable conformations in different PDB
files.
The authors of the database is:
Dr. Weizhong Li et al.
of the
Molecular design lab