[ccp4bb] Building sugars
Dear all, What's the correct way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar ligands in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund
Re: [ccp4bb] Building sugars
Dear Folmer, I build them from monomers like NAG, MAN, FUC etc. It used to be quite messy (reason why people put in triscaccharides??) but works fine nowadays. You have to put in LINK records to specify the connections and remove the oxygen which gets replaced by the link (usually O1). There should be plenty of files like that in pdb (like 4az3, which I deposited recently...). Good luck! Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Building sugars Dear all, What's the correct way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar ligands in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund
Re: [ccp4bb] Building sugars
Concerning the naming as one molecule: the sugar monomers get the same chain ID as the protein they are connected to and arbitrary residue numbers. I usually start numbering from 1000 to prevent overlap with the numbering of the amino acids. HS. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Building sugars Dear all, What's the correct way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar ligands in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund
Re: [ccp4bb] Building sugars
Hi Folmer, Just to add some tips: Concerning the naming as one molecule: the sugar monomers get the same chain ID as the protein they are connected to and arbitrary residue numbers. I usually start numbering from 1000 to prevent overlap with the numbering of the amino acids. 1) Just don't use insertion codes, some people find it upsetting ;) And keep the residue numbering consistent between NCS copies. 2) The glycosciences.de portal has many tools for dealing with carbohydrates: http://www.glycosciences.de/ I really like PDB-care and CARP for validation in the building and refinement process. 3) When using TLS you should try to figure out whether it's useful to add the sugars to the group of the linked protein residue or to have specific groups for your sugar trees. Cheers, Robbie HS. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Building sugars Dear all, What's the correct way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar ligands in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund
Re: [ccp4bb] Building sugars
Hi all Thank you all for your replies. I might have expressed myself poorly, but I am not talking about covalently linked sugar modifications, so for my purpose there's no need to be concerned about insertion codes ;-) The glycosciences.de link is really useful. There does not seem to be a test to verify correct PDB nomenclature though. Or perhaps RAF (for raffinose, a tri-saccharide) is OK to use? Best regards, Folmer 2013/2/21 Robbie Joosten robbie_joos...@hotmail.com Hi Folmer, Just to add some tips: Concerning the naming as one molecule: the sugar monomers get the same chain ID as the protein they are connected to and arbitrary residue numbers. I usually start numbering from 1000 to prevent overlap with the numbering of the amino acids. 1) Just don't use insertion codes, some people find it upsetting ;) And keep the residue numbering consistent between NCS copies. 2) The glycosciences.de portal has many tools for dealing with carbohydrates: http://www.glycosciences.de/ I really like PDB-care and CARP for validation in the building and refinement process. 3) When using TLS you should try to figure out whether it's useful to add the sugars to the group of the linked protein residue or to have specific groups for your sugar trees. Cheers, Robbie HS. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Building sugars Dear all, What's the correct way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar ligands in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund -- Folmer Fredslund
Re: [ccp4bb] Building sugars
Hi Folmer, RAF is in the PDB ligand dictionary with status 'REL' so you can use it. If RAF is a subset of something bigger, then perhaps you should use monosaccharide building blocks. If in doubt, ask a PDB annotator. Anyway, PDB-care will check whether the connectivity in a compound named RAF matches the standard description of RAF. CARP will check the torsion angles between the monosaccharide building blocks. HTH, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 15:37 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Building sugars Hi all Thank you all for your replies. I might have expressed myself poorly, but I am not talking about covalently linked sugar modifications, so for my purpose there's no need to be concerned about insertion codes ;-) The glycosciences.de link is really useful. There does not seem to be a test to verify correct PDB nomenclature though. Or perhaps RAF (for raffinose, a tri- saccharide) is OK to use? Best regards, Folmer 2013/2/21 Robbie Joosten robbie_joos...@hotmail.com Hi Folmer, Just to add some tips: Concerning the naming as one molecule: the sugar monomers get the same chain ID as the protein they are connected to and arbitrary residue numbers. I usually start numbering from 1000 to prevent overlap with the numbering of the amino acids. 1) Just don't use insertion codes, some people find it upsetting ;) And keep the residue numbering consistent between NCS copies. 2) The glycosciences.de portal has many tools for dealing with carbohydrates: http://www.glycosciences.de/ I really like PDB-care and CARP for validation in the building and refinement process. 3) When using TLS you should try to figure out whether it's useful to add the sugars to the group of the linked protein residue or to have specific groups for your sugar trees. Cheers, Robbie HS. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Building sugars Dear all, What's the correct way to build and refine sugar polymers? I am currently building several structures with different kinds of sugar polymers bound to them. Searching for similar ligands in the PDB, I end up with e.g. trisaccharides that are named as one molecule, even though they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund -- Folmer Fredslund
