PSCDB

2016/11/30

Web 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
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. PSCID List
  3. Protein Structural Change Data
  4. Protein 3D Structure Image
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "PSCDB" data.
File README_e.html (English)
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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 itemDescription
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
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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 itemDescription
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")
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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)
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3. License

Last updated : 2016/11/30

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.

 

Creative Commons License

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:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. 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:

  1. 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.
  2. 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).
  3. 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.

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4. Update History

DateUpdate 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.
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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

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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

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