Jacob Keller
There is a service that will hopefully do the calculation you want,
search for a template of
residues (eg. catalytic-triads). This is just a through space
superposition of atoms.
It is part of a tool set of fragments found by knowledge based analysis
(pdbetemplate) ....
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/
and there is a tool called DB search accessible from this page , or
directly from here...
http://www.ebi.ac.uk/pdbe-as/pdbesearch/PDBeSearch.jsp
You can upload a small template of residues (up to 6) in PDB format
using the
[upload and analyse] button. The search is weighted based
on occupancy - where weights for each atom a defined by the occupancy value.
You can specify to just the CA atoms, the side chain (based on
occupancy), and
use fuzzy matching (slow) where ASP looks like GLU etc.
Here is an example PDB file fragment you can use to try out the search - it
is a catalytic quartet of residues - a superset of the catalytic triad.
Regards
Tom Oldfield, PDBe.
HEADER HYDROLASE (SERINE PROTEINASE) 22-JAN-85 5CHA
5CHA 3
COMPND ALPHA CHYMOTRYPSIN A (E.C.3.4.21.1)
5CHA 4
SOURCE COW (BOS $TAURUS)
5CHA 5
AUTHOR R.A.BLEVINS,A.TULINSKY 5CHA 6
SITE 1 CTA 3 HIS A 57 ASP A 102 SER A 195
5CHA 160
ATOM 403 N HIS A 57 28.981 28.453 20.681 1.00 10.49
5CHA 550
ATOM 404 CA HIS A 57 28.691 28.510 22.151 1.00 10.51
5CHA 551
ATOM 405 C HIS A 57 29.897 28.096 22.990 1.00 11.71
5CHA 552
ATOM 406 O HIS A 57 29.926 28.441 24.252 1.00 11.27
5CHA 553
ATOM 407 CB HIS A 57 27.441 27.724 22.518 1.00 10.23
5CHA 554
ATOM 408 CG HIS A 57 27.711 26.268 22.692 1.00 11.48
5CHA 555
ATOM 409 ND1 HIS A 57 27.449 25.299 21.720 1.00 11.56
5CHA 556
ATOM 410 CD2 HIS A 57 28.206 25.605 23.753 1.00 10.62
5CHA 557
ATOM 411 CE1 HIS A 57 27.787 24.143 22.229 1.00 12.29
5CHA 558
ATOM 412 NE2 HIS A 57 28.219 24.290 23.459 1.00 12.00
5CHA 559
ATOM 729 N ASN A 100 21.139 29.092 17.682 1.00 15.17
5CHA 876
ATOM 730 CA ASN A 100 21.091 28.846 16.199 1.00 14.91
5CHA 877
ATOM 731 C ASN A 100 22.361 29.384 15.589 1.00 14.15
5CHA 878
ATOM 732 O ASN A 100 22.993 30.366 16.007 1.00 14.62
5CHA 879
ATOM 733 CB ASN A 100 19.865 29.473 15.542 1.00 14.99
5CHA 880
ATOM 734 CG ASN A 100 19.459 28.894 14.195 1.00 15.90
5CHA 881
ATOM 735 OD1 ASN A 100 19.768 27.721 13.910 1.00 15.64
5CHA 882
ATOM 736 ND2 ASN A 100 18.776 29.679 13.303 1.00 15.91
5CHA 883
ATOM 745 N ASP A 102 25.217 27.828 15.245 1.00 8.90
5CHA 892
ATOM 746 CA ASP A 102 26.263 27.454 16.230 1.00 8.03
5CHA 893
ATOM 747 C ASP A 102 27.602 26.986 15.681 1.00 7.56
5CHA 894
ATOM 748 O ASP A 102 28.030 25.875 15.937 1.00 6.97
5CHA 895
ATOM 749 CB ASP A 102 25.612 26.547 17.282 1.00 7.61
5CHA 896
ATOM 750 CG ASP A 102 26.373 26.259 18.576 1.00 7.61
5CHA 897
ATOM 751 OD1 ASP A 102 26.215 25.289 19.348 1.00 6.70
5CHA 898
ATOM 752 OD2 ASP A 102 27.250 27.077 18.886 1.00 7.66
5CHA 899
ATOM 1404 N SER A 195 30.503 18.936 23.287 1.00 10.84
5CHA1551
ATOM 1405 CA SER A 195 30.268 20.144 22.534 1.00 11.39
5CHA1552
ATOM 1406 C SER A 195 31.398 20.500 21.546 1.00 11.49
5CHA1553
ATOM 1407 O SER A 195 32.602 20.510 21.836 1.00 10.92
5CHA1554
ATOM 1408 CB SER A 195 30.081 21.398 23.463 1.00 11.44
5CHA1555
ATOM 1409 OG SER A 195 28.708 21.332 23.826 1.00 13.00
5CHA1556
On 27/06/14 21:49, Keller, Jacob wrote:
> I have wanted for some time to search for catalytic-triad-like configurations by defining three Ca-Cb bonds from known catalytic triads, then searching the pdb for matches, but have not thought of a quick and/or easy way to do this--can your software do this sort of thing, or is there some other software which could be used for this?
>
> JPK
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Dale Tronrud
> Sent: Friday, June 27, 2014 4:27 PM
> To: [log in to unmask]
> Subject: [ccp4bb] New Version of the Protein Geometry Database Now Available
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Protein Geometry Database Server V 1.0
> http://pgd.science.oregonstate.edu/
> Developed by Andy Karplus' laboratory at Oregon State University
>
> We are pleased to announce the availability of an enhanced version of the Protein Geometry Database (PGD) web service, originally announced in Berkholz et al (2010) Nucleic Acids Research 38, D320-5.
> This server allows you to explore the many backbone and side chain conformations that exist in the PDB as well as the protein geometry (lengths and angles) that occur in those conformations. This service is ideal for finding instances of particular conformations or peculiar bond lengths or angles. It is also quite adept at identifying sets of fragments that can then be examined for systematic variation in "ideal" geometry. The expanded PGD now includes all conformational and covalent geometry information not just for the backbone but also for the sidechains.
>
> There are three basic operations available: selecting a set of fragments via a delimited search, analyzing the geometry of those fragments, and dumping the results to your computer for more specialized analysis.
>
> To control bias in statistical analyses due to the variable number of entries with the same or similar sequence, the database contains only the highest quality model in each sequence cluster as identified by the Pisces server from Roland Dunbrack's lab. Two settings, 90% and 25% sequence identity, are available. Currently, at the 90% sequence identity level there are 16,000 chains and at the 25% level this drops to about 11,000 chains.
>
> You can filter a search based on the quality of the model as indicated by resolution and R values. A search can also be filtered based on DSSP secondary structure, amino acid type, the phi/psi/omega angles and bond lengths, angles, and chi angles. For example, you can find all cysteine residues in the center of three-residue peptide fragments (i.e. not at a peptide terminus), in beta sheet, with both peptide bonds trans, and CB-SG length greater than 1.85 A from models with resolution better than 1.5 A. By the way, in the "no more than 25% sequence identity" category there are 25 of them.
>
> Once you have a set of results, you can create 2D plots showing the relationships of up to three features (i.e. bond lengths, bond angles, or conformational angles). For instance, you can look at how a given feature varies with phi and psi using a phi(i)/psi(i) plot. Or, you can just as easily look at the variation with psi(i)/phi(i+1), or even the relationships between any selected bond angles. As one example, it is instructive to perform a default search and plot NCaCb vs NCaC colored based on CbCaC. As this search is restricted to just the highest resolution models, you can see the justification for chiral volume restraints.
>
> Finally, all of your results can be downloaded for your own analysis.
>
> Development of the PGD continues. If you have worked with the site and have any ideas and suggestions for how to improvement it, please drop us a line.
>
> The publication describing the PGD is:
>
> Berkholz, D.S., Krenesky, P.B., Davidson, J.R., & Karplus, P.A.
> (2010) Protein Geometry Database: A flexible engine to explore backbone conformations and their relationships with covalent geometry.
> Nucleic Acids Res. 38, D320-5.
>
> Also, some examples of published analyses enabled by earlier versions of the PGD are listed here:.
>
> Berkholz, D.S., Shapovalov, M.V., Dunbrack, R.L.J. & Karplus, P.A.
> (2009). Conformation dependence of backbone geometry in proteins.
> Structure 17, 1316-1325.
>
> Hollingsworth, S.A., Berkholz, D.S. & Karplus, P.A. (2009). On the occurrence of linear groups in proteins. Protein Science 18, 1321-1325
>
> Hollingsworth, S.A. & Karplus, P. A. (2010). Review: A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. BioMolecular Concepts 1, 271-283.
>
> Berkholz, D.S., Driggers, C.M., Shapovalov, M.V., Dunbrack, R.L., Jr.
> & Karplus P.A. (2012) Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A. 109, 449-53.
>
> Dale Tronrud & P. Andrew Karplus
> Department of Biochemistry and Biophysics Oregon State University -----BEGIN PGP SIGNATURE-----
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> Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
>
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> B1IAn0Q5xx8ptRosgMXswdYmdjNKyFkA
> =D63d
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--
Tom Oldfield , PhD
Team Leader
Head of PDBe Databases and Services
Protein Databank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Gemome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel : ++44 (0) 1223 492526
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