PSCDB
2016/11/30Web Site: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/pscdb/
This database is to represent the relationship between protein structural change and ligand binding.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
|---|---|
| Description of data contents | HTML file to describe "PSCDB" data. |
| File | README_e.html (English) |
2.2 PSCID List
| Data name | PSCID List |
|---|---|
| Description of data contents | The list of PSCID and common elements of each entry |
| File | pscdb_pscid_list.zip (24.4 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| PSCID | ID of this data |
| Classification | The six digit numbers (from left to right) are, respectively, 1st: the number of components of motion for the coupled domain motion 2nd: the number for the independent domain motion 3rd: the number for the coupled local motion 4th: the number for the independent local motion 5th: the number of domains exhibiting the burying ligand motion 6th: the number of domains with ligand molecules situated on the protein surface. |
| Protein name | Protein name |
| FreeID | PDB ID of ligand-free form |
| BoundID | PDB ID of ligand-bound form |
| Ligands | Ligand name(PDB) |
| EC | Enzyme commission number |
| Distance | The distance between the active site annotated in Catalytic Site Atlas (CSA) and the ligand-binding sites |
2.3 Protein Structural Change Data
| Data name | Protein Structural Change Data |
|---|---|
| Description of data contents | This data represent the relationship between protein structural change and ligand binding. |
| File | pscdb.zip (45.6 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| PSCID | ID of this data |
| Classification | The six digit numbers (from left to right) are, respectively, 1st: the number of components of motion for the coupled domain motion 2nd: the number for the independent domain motion 3rd: the number for the coupled local motion 4th: the number for the independent local motion 5th: the number of domains exhibiting the burying ligand motion 6th: the number of domains with ligand molecules situated on the protein surface. |
| Protein name | Protein name |
| FreeID | PDB ID of ligand-free form |
| BoundID | PDB ID of ligand-bound form |
| Ligands | Ligand name(PDB) |
| EC | Enzyme commission number |
| Distance | The distance between the active site annotated in Catalytic Site Atlas (CSA) and the ligand-binding sites |
| Component No | Component Number |
| Type of motion | Type of motion |
| Ligand binding | Type of ligand binding |
| Type of coupled motion | Type of coupled motion |
| Order-disorder transition | Whether the open form contains the disordered structure. ("Yes" or space) |
| RMSD | The root-mean-square displacement of a component of motion calculated for the domain motions |
| Mean displacement | The mean displacement of a component of motion calculated for the local motions |
| C.C. | The correlation coefficient between the displacement vector predicted by the linear response theory and the one observed in the crystal structures |
| Crystal packing | Whether the change in the crystal environment is coupled with the structural change. ("Coupled" or space) |
| Fixed segment | Fixed segment |
| Moving segment | Moving segment |
| Disorder | The number of disordered residues |
| Helix/coil | The number of residues exhibiting the alpha-helix to coil transition |
| Open state | Distinction between the open state and the closed state required for examining the influence of the crystal environment |
| H-bonds/ligand | The number of hydrogen-bonds with ligands (observed in the proteins classified in "Buried Ligand") |
| H-bonds/water | The number of hydrogen-bonds with water (observed in the proteins classified in "Buried Ligand") |
| H-bonds/protein | The number of hydrogen-bonds with proteins (observed in the proteins classified in "Buried Ligand") |
2.4 Protein 3D Structure Image
| Data name | Protein 3D Structure Image |
|---|---|
| Description of data contents | Protein 3D structure images created with PyMOL |
| File | pscdb_image.zip (96.4 MB) |
3. License
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "PSCDB © Amemiya Takayuki (The Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)) licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
The Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)
Takayuki Amemiya
E-mail: pscdb-admin[at]force[dot]cs[dot]is[dot]nagoya-u[dot]ac[dot]jp
About Providing Links to This Database
You can freely provide links to all contents in this database. But, contents might be changed without notice.
4. Update History
| Date | Update contents |
|---|---|
| 2016/11/30 | PSCDB English archive site is opened. |
| 2011/11/13 | PSCDB (http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/) is opened. |
5. Literature
T. Amemiya, R. Koike, A. Kidera, and M. Ota.PSCDB: a database for protein structural change upon ligand binding.
2012, Nucleic Acids Res., 40, D554-D558.
PMID: 22080505
6. Contact address
When you have any question about "PSCDB", contact the following:The Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)
Takayuki Amemiya
E-mail: pscdb-admin[at]force[dot]cs[dot]is[dot]nagoya-u[dot]ac[dot]jp