Bachar Cheaib wrote: > This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC" does > not tell us if a structure is really multi > or monomeric in the pdb file. > Right, that tells you what it is in vivo. To see what it is in the pdb file, i.e. contents of the asymmetric unit, look at the "compound" records near the top:
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RXR-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN (LBD); COMPND 5 SYNONYM: RETINOID X RECEPTOR LIGAND-BINDING DOMAIN, 9-CIS RETINOIC COMPND 6 ACID; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1; COMPND 10 CHAIN: E, F; COMPND 11 SYNONYM: NCOA-1, STEROID RECEPTOR COACTIVATOR-1, SRC-1, RIP160, HIN-2 COMPND 12 PROTEIN; COMPND 13 EC: 2.3.1.48; COMPND 14 ENGINEERED: YES You have an entry MOL_ID for each distinct protein. In this case there are two. For each of these MOL_ID's there will be one or more chains, in this case A,B are the receptor and E,F are the coactivator. From this you would conclude that the pdb contains a honmodimer of heterodimers, or posibly a heterodimer of homodimers, if the distinction makes any sense. In the simplest case there will be only one kind of subunit and the number of chains for it is the nember of protomers in the ASU. More complicted; the protomer could have non-integral ratios of subunits, like F1 ATPase alpha(3) beta(3) gamma(1) and then multiple of these protomers in the ASU. Then I guess the minimum number of chains in a subunit would be the number of protomers in the ASU Or going with a web browser to the page for that structure, select the link "display files" then "FASTA fles" and see how many times each sequence is repeated. ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
