tag:blogger.com,1999:blog-7844526396210378482.post7736128040105897771..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: How to get an experimental ligand structure from the PDB? Part 2Noel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-7844526396210378482.post-31252132189613916652010-06-17T16:38:15.768+01:002010-06-17T16:38:15.768+01:00ExtractFromPDBFiles from MayaChemTools should work...ExtractFromPDBFiles from MayaChemTools should work fine.<br />1. Extract all HETATM<br />2. Remove all of the artifacts (sulfate ions, Na, Cl, etc).Vladimir Chupakhinhttps://www.blogger.com/profile/14838130425318070954noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-29953270747448143402010-06-11T16:24:01.910+01:002010-06-11T16:24:01.910+01:00Understood. If this is common practice, then the p...Understood. If this is common practice, then the problem is that the PDB should *know* that this is a single ligand, and should output it and display it accordingly.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-2721223083261714472010-06-11T12:25:00.906+01:002010-06-11T12:25:00.906+01:00For labeling parts of molecules as amino acids, it...For labeling parts of molecules as amino acids, it is frequently useful for peptidomimetics to have things labelled that way, or break up an inhibitor into parts that correspond to residues. It makes it much easier to understand the drug, even if it makes cheminformatics more difficult.<br /><br />That said, they usually label the amino acids as HETATM records, not ATOM records. (You can look up any amino acid and see this, eg http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=LEU says "Free Ligand in 57 structures", any of these will have a HETATM LEU)<br /><br />I just wanted to say that while it looks silly in these cases, there are a ton of places in the PDB where having things this way is extremely useful. A blanket conversion of these types of cases into single residues would lose a lot of information.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-59069989348887742132010-06-11T09:51:48.991+01:002010-06-11T09:51:48.991+01:00I saw that remark, but I don't know if the sta...I saw that remark, but I don't know if the statement about the missing hetereoatom is even correct. The structure I see in the PDB corresponds to the one in the paper.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-75365355541434530482010-06-11T08:15:47.452+01:002010-06-11T08:15:47.452+01:00not so easy to find other examples :(not so easy to find other examples :(Matteo Florishttps://www.blogger.com/profile/13177555699430611910noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-26365286169957790472010-06-10T17:45:01.480+01:002010-06-10T17:45:01.480+01:00Really really nice!
Tomorrow I'll try to find ...Really really nice!<br />Tomorrow I'll try to find more ambiguities...<br />how to do it?<br />If you have a look at the PDB file of 1PPH entry, you can read this:<br /><br /><i><br />REMARK 600 3-TAPAP, A SYNTHETIC THROMBIN INHIBITOR, IS NONCOVALENTLY <br />REMARK 600 BOUND TO THE ACTIVE SITE. <br />REMARK 600 <br />REMARK 600 A CALCIUM CAL 480 AND A SULFATE SO4 ARE ADDITIONALLY <br />REMARK 600 PRESENT. <br />REMARK 600 <br />REMARK 600 3-TAPAP "RESIDUES" (NOMENCLATURE SEE PAPER) ARE TOS I 1, <br />REMARK 600 APM I 2, PIP I 3. <br />REMARK 610 <br />REMARK 610 MISSING HETEROATOM <br />REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; <br />REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; <br />REMARK 610 I=INSERTION CODE): <br />REMARK 610 M RES C SSEQI <br />REMARK 610 APM E 2 <br /></i><br /><br />maybe this is a common remark... let's see.Matteo Florishttps://www.blogger.com/profile/13177555699430611910noreply@blogger.com