Re: [ccp4bb] Unidentified ligand (electron density) found at active site
Hi, Why is it that you are so reluctant to identify this compound as Ser-Gly? Its fit to the density is great. To wax historical, we saw unexpected density in the active site of apo Thermolysin. It appeared to be Val-Ala, but with refinement it developed into Val-Lys. It happens that Val-Lys are the last two residues of the protein. Residues 315 and 316 were present at full occupancy in the crystal so I presume the peptide was clipped off molecules that didn't crystallize. Of course proving that the density actually represents Ser-Gly, or any other compound you decide upon is much harder than building a model to fit the density. What is harder than identifying a bit of density, is coming up with an experiment to prove it. Dale Tronrud Ronaldo Alves Pinto Nagem wrote: Dear CCP4bb users, As suggested by some users, I am attaching to this email the electron density of the unidentified ligand. As I mentioned before it looks like a dipeptide GlySer, but we are still in doubt. Attempts to correlate with the protein function are being done. One might see in the pictures that the ligand coordinate a metal ion. Cheers Ronaldo. - Prof. Dr. Ronaldo Alves Pinto Nagem Universidade Federal de Minas Gerais Instituto de Ciências Biológicas Departamento de Bioquímica e Imunologia Av. Antônio Carlos, 6627 - Caixa Postal 486 Bairro Pampulha - CEP: 31270-901 Belo Horizonte, MG - Brasil Tel: +55 31 3499-2626 Fax: +55 31 3499-2614 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Unidentified ligand (electron density) found at active site
I learned from an earlier CCP4BB post of a routine in Phenix that searches a database of small molecules from (I think) 200 protein-small molecule complex structures. Some of the small molecules seemed redundant; however, they may be in different conformations in the different structures that are used. From the Phenix GUI, click on the Strategies menu, and then go to the ligand sub-menu, and choose ligand identification. Gregg *** Gregg Crichlow Department of Pharmacology Yale University Box 208066 New Haven, CT 06520-8066 *** -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ronaldo Alves Pinto Nagem Sent: Friday, November 30, 2007 7:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unidentified ligand (electron density) found at active site Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound – I do not know its atom composition)? I hope someone could help. Thanks Ronaldo.
Re: [ccp4bb] Unidentified ligand (electron density) found at active site
Did you had an inhibitor present in your purification ? Complete tablets ? Can you derive from the chemical environment perhaps if some of the atoms are nitrogens or oxygens ? Then you could sketch your putative molecule and search in the NCI database for homologous structures to your sketch. Here's the link: http://dtp.nci.nih.gov Juergen Ronaldo Alves Pinto Nagem wrote: Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound – I do not know its atom composition)? I hope someone could help. Thanks Ronaldo. -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] Unidentified ligand (electron density) found at active site
If you send a picture of this stuff to the list, I bet someone may recognize it :) I think it's called 'distributed computing'. On a more serious note, a pharmacophore matching routine would do what you need, but you'd have to convert from E.D. to a 'blank' pharmacophore with all property parameters set exactly to 1. Unfortunately, I don't know of any non-commercial programs for that stuff... Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ronaldo Alves Pinto Nagem Sent: Friday, November 30, 2007 7:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unidentified ligand (electron density) found at active site Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound - I do not know its atom composition)? I hope someone could help. Thanks Ronaldo.
[ccp4bb] Unidentified ligand (electron density) found at active site
Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound – I do not know its atom composition)? I hope someone could help. Thanks Ronaldo.
Re: [ccp4bb] Unidentified ligand (electron density) found at active site
If you can narrow down the possibilities of compounds to a list of a few - let's say not more than 20...30 - then ARP/wARP 7 might be of help. It has a ligand building tool. One of its protocols is building an unidentified ligand from a list. Check the user-guide for detailed information on the usage. Regards, Gerrit. Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound â I do not know its atom composition)? I hope someone could help. Thanks Ronaldo. - This mail sent through IMP: http://horde.org/imp/
