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Methylation on K-552 in P13538

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Methylation on K-552 in P13538

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N-linked Glycosylation on N-361 in P00533

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N-linked Glycosylation on N-361 in P00533

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Methylation on C-369 in P00877

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Methylation on C-369 in P00877

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Phosphorylation on T-190 in Q9Y6E0

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Phosphorylation on T-190 in Q9Y6E0

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N-linked Glycosylation on N-279 in P15848

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N-linked Glycosylation on N-279 in P15848

Example Frame


Welcome to the Post Translational Modification Structural Database (PTM-SD).

Proteins are composed of a succession of amino acid residues. Their 3D structures are the support of major crucial biological functions.

Post translational modifications (PTMs) are covalent chemical modifications of proteins that typically occur after the protein synthesis.

They allow a fine and sometimes obligatory modulation of biological functions; they can determine proteins activity state, localization, turnover, and interactions with other proteins.

PTM-SD provides an access to proteins for which PTMs are both experimentally annotated and structurally resolved.

Read more...

We have used different databases to characterize the different PTMs resolved in the protein structures (see HELP page and the FLOWCHART for details on the difficulty to define them properly):

Protein structures are found in Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) [ref]

Sequences contained in PDB were compared with sequences of UniProt database (http://www.uniprot.org/) [ref]

PTMs found in the protein structures were compared with PTMs annotated in dbPTM (http://dbptm.mbc.nctu.edu.tw/) [ref] and PTMCuration (http://selene.princeton.edu/PTMCuration/) [ref]




Browse    Database
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(Press Ctrl to multiple selection)

P D B - I D

U n i P r o t - A C O R G A N I S M P T M

MODIFIED AMINO ACID SECONDARY STRUCTURE ON PTM LOCATION SCOP CLASSIFICATION OF PROTEIN


ANNOTATION FOUND IN MODRES PDB RECORDS

Note:

This filter refers to the annotations found in the MODRES PDB reccords.

ANNOTATION FOUND IN dbPTM

Note:

This filter refers to the experimental sequence annotations taken from dbPTM.

In a limited number of case the selected PTMs of the list could be different from the one observed in the 3D structure. Please check.
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Tools
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Compute pie chart of organism distribution, protein distribution and PTM annotation distribution.

(Read more...)

Compute local structure entropy at the surrounding positions of PTM sites.

(Read more...)

Compute dendogram and histogram of pairwise sequence identity of selected proteins.

(Read more...)

Create    Your    Dataset
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First Browse     Database and select the PTMs of interest. Then use Tools to minimize redundancy. Finally click Here to download your dataset.


Contact


Pierrick
Craveur

Joseph
Rebehmed

Alexandre G.
de Brevern		 
	This webserver has been designed by Pierrick Craveur, Joseph Rebehmed and Alexandre G. de Brevern.

	PTM-SD program and the database implementation has been written mainly by Pierrick Craveur, with help of Dr. Joseph Rebehmed.
	Pierrick Craveur had designed the database architecture.
	Dr. Joseph Rebehmed and Dr. Alexandre G. de Brevern conceived the study with Pierrick Craveur.
	All members have extensively tested the database and manually curated the PDB entries.

	We all belong to DSIMB lab in Paris :

	INSERM UMR-S 665,
	DSIMB,
	Universite Paris Diderot - Paris 7,
	INTS,
	6, rue Alexandre Cabanel
	75739 Paris Cedex 15, FranceYou can contact us by mail :
	

	
pierrick.craveur (at) inserm.fr[ curriculum vitae ].

	
joseph.rebehmed (at) inserm.fr[ personal website ].

	
alexandre.de-brevern (at) inserm.fr[ personal website ].

Links 
		

		You can also look at other tools developed by our team :
		

		

		[ VLDPws ]			(Esque, Leonard, de Brevern and Oguey, Nucleic Acid Res, 2013).
		[ mulPBA ]			(Leonard, Jospeh, Srinivasan, Gelly et de Brevern, J Biol Struct Dyn, 2013).
		[ PredyFlexy ]			(de Brevern, Bornot, Craveur, Etchebest and Gelly, Nucleic Acid Res , 2012).
		[ iPBA ]			(Gelly, Joseph, Srinivasan et de Brevern., Nucleic Acid Res , 2011).
		[ Protein Peeling 3D ]		(Gelly and de Brevern, Bioinformatics , 2011).
		[ LocPred ]			(de Brevern et al., In Silico Biology , 2004).
		

	

	

		Databases related to Post-Translational Modifications: 
		
		More general databases :
		

		

		PTMcode: 			https://ptmcode.embl.de/
		dbPTM: 				https://dbptm.mbc.nctu.edu.tw/
		PTM Statistics Curator: 	https://selene.princeton.edu/PTMCuration/
		PHOSIDA : 			https://www.phosida.com/
		PHOSPHOSITE: 			https://www.phosphosite.org/homeAction.do
		PHOSPHOelm: 			https://phospho.elm.eu.org/
		OglycBase: 			https://www.cbs.dtu.dk/databases/OGLYCBASE/
	
		PDB : 		https://www.rcsb.org/pdb/home/home.do
		uniprot : 	https://www.uniprot.org/
		HPRD: 		https://www.hprd.org/
	

	

		

		We also acknowledge :
		

		

					French National Institute for Health and Medical Research (INSERM)


					Université Paris Diderot - Paris 7


						Sorbonne Paris Cité


						French National Institute For Blood Transfusion


						Laboratoire d'Excellence GR-Ex


				DSIMB , UMR_S 665