Eugenio, A quick search at the PDB web site for 'cyclodextrin' yields :- <cut&paste> # 3DB database, Wed Jul 1 16:19:17 EDT 1998 # Query: dat=dep&ex=xrd+or+nmr&kw=cyclodextrin&m=du # Hits: 17 (search time 8 sec) 1A47 Cgtase From Thermoanaerobacterium Thermosu... Uitdehaag 2.56 1AC0 Glucoamylase, Granular Starch-Binding Doma... Sorimachi 1ACZ Glucoamylase, Granular Starch-Binding Doma... Sorimachi 1BTC Beta-Amylase with Alpha-Cyclodextrin (Alph... Mikami 2.00 1CDG Cyclodextrin Glycosyltransferase (Cgtase) Lawson 2.00 1CGT Cyclodextrin Glycosyltransferase Klein 2.00 1CGU Cyclodextrin Glycosyltransferase mutant As... Klein 2.50 1CIU Thermostable Cgtase From Thermoanaerobacte... Knegtel 2.30 1CXE Complex Of Cgtase With Maltotetraose At Ro... Knegtel 2.10 1CXF Complex Of A (D229n E257q) Double Mutant C... Knegtel 2.60 1CXH Complex Of Cgtase With Maltotetraose At Ro... Knegtel 2.40 1CXI Wild-Type Cgtase From Bacillus Circulans S... Knegtel 2.20 1CYG Cyclodextrin Glucanotransferase (Cgtase) Kubota 2.50 1DIJ Complex Of A Y195f Mutant Cgtase From B. C... Strokopytov 2.60 1PAM Cyclodextrin Glucanotransferase Harata 1.80 1TCM Cyclodextrin Glycosyltransferase W616a Mut... Knegtel 2.20 3CGT Cyclodextrin Glycosyltransferase with Its ... Schmidt 2.40 </cut&paste> but examining all the heterogroups in the structures that are complexes only finds (in 3CGT) BETA-CYCLODEXTRIN CYCLO-HEPTA-AMYLOSE the coordinates of which I attach, and which can also be seen at http://www.pdb.bnl.gov/pdb-bin/send-het?BCD with a chime-enabled web browser. Hope this helps. Best Rgds., Alan Mills at Venus Internet Ltd, 24 Denmark Street, London WC2H 8NJ, UK email:alan@venus.co.uk web:http://www.venus.co.uk Tel: +44 (0)171 240 5858 Fax: +44 (0)171 240 5859 Providing Web and Internet services and solutions On Wed, 1 Jul 1998, Eugenio Alvarado wrote:
Date: Wed, 1 Jul 1998 13:29:09 -0600 From: Eugenio Alvarado <ealva@ns.equi.ucr.ac.cr> To: chemweb@ic.ac.uk Subject: cyclodextrin.pdb
Hi,
Does anyone have cyclodextrin (alpha, beta or gamma) in pdb or similar format? If so, I will greatly appreciate it if you send me the file or the URL where I can find it. So far, I have looked in several databanks and the only one file I have found is a cyclic heptamer of BETA!!! (1-4) glucose.
Thank you,
------------------------------------------------------------ Dr. Eugenio Alvarado ealva@ns.equi.ucr.ac.cr Escuela de Quimica Tel: (506) 207-5038 Universidad de Costa Rica Fax: (506) 253-5020 San Jose, COSTA RICA ------------------------------------------------------------
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COMPND BCD BETA-CYCLODEXTRIN REMARK BCD Extracted from PDB file 1dmb.pdb REMARK BCD Formula C42 H70 O35 REMARK BCD Nr of non-hydrogen atoms 77 REMARK BCD Residue type BCD REMARK BCD Residue name 180 REMARK BCD Original residue name (for O) $371 REMARK BCD RESOLUTION. 1.80 ANGSTROMS. 1DMB 32 REMARK BCD HETATM 1 C11 BCD 180 -3.833 4.636 -2.253 1.00 20.00 HETATM 2 C21 BCD 180 -2.960 5.127 -3.436 1.00 20.00 HETATM 3 O21 BCD 180 -3.430 4.515 -4.655 1.00 20.00 HETATM 4 C31 BCD 180 -1.485 4.844 -3.181 1.00 20.00 HETATM 5 O31 BCD 180 -0.677 5.445 -4.216 1.00 20.00 HETATM 6 C41 BCD 180 -1.057 5.388 -1.831 1.00 20.00 HETATM 7 O41 BCD 180 0.251 4.864 -1.577 1.00 20.00 HETATM 8 C51 BCD 180 -1.982 4.928 -0.711 1.00 20.00 HETATM 9 O51 BCD 180 -3.371 5.282 -1.067 1.00 20.00 HETATM 10 C61 BCD 180 -1.744 5.561 0.639 1.00 20.00 HETATM 11 O61 BCD 180 -2.606 4.932 1.601 1.00 20.00 HETATM 12 C12 BCD 180 1.249 5.731 -1.138 1.00 20.00 HETATM 13 C22 BCD 180 2.529 5.551 -1.962 1.00 20.00 HETATM 14 O22 BCD 180 2.186 5.713 -3.347 1.00 20.00 HETATM 15 C32 BCD 180 3.176 4.223 -1.624 1.00 20.00 HETATM 16 O32 BCD 180 4.407 4.113 -2.362 1.00 20.00 HETATM 17 C42 BCD 180 3.467 4.152 -0.127 1.00 20.00 HETATM 18 O42 BCD 180 4.021 2.866 0.165 1.00 20.00 HETATM 19 C52 BCD 180 2.176 4.577 0.658 1.00 20.00 HETATM 20 O52 BCD 180 1.518 5.524 0.240 1.00 20.00 HETATM 21 C62 BCD 180 2.313 4.369 2.144 1.00 20.00 HETATM 22 O62 BCD 180 0.979 4.063 2.537 1.00 20.00 HETATM 23 C13 BCD 180 5.345 2.683 0.586 1.00 20.00 HETATM 24 C23 BCD 180 5.930 1.473 -0.143 1.00 20.00 HETATM 25 O23 BCD 180 5.725 1.650 -1.573 1.00 20.00 HETATM 26 C33 BCD 180 5.237 0.204 0.302 1.00 20.00 HETATM 27 O33 BCD 180 5.815 -0.918 -0.396 1.00 20.00 HETATM 28 C43 BCD 180 5.309 0.042 1.799 1.00 20.00 HETATM 29 O43 BCD 180 4.493 -1.058 2.147 1.00 20.00 HETATM 30 C53 BCD 180 4.720 1.284 2.471 1.00 20.00 HETATM 31 O53 BCD 180 5.369 2.450 1.991 1.00 20.00 HETATM 32 C63 BCD 180 4.946 1.230 4.004 1.00 20.00 HETATM 33 O63 BCD 180 4.763 2.386 4.712 1.00 20.00 HETATM 34 C14 BCD 180 4.898 -1.963 3.166 1.00 20.00 HETATM 35 C24 BCD 180 5.460 -3.219 2.428 1.00 20.00 HETATM 36 O24 BCD 180 6.614 -2.900 1.676 1.00 20.00 HETATM 37 C34 BCD 180 4.343 -3.728 1.520 1.00 20.00 HETATM 38 O34 BCD 180 4.808 -4.794 0.689 1.00 20.00 HETATM 39 C44 BCD 180 3.172 -4.134 2.385 1.00 20.00 HETATM 40 O44 BCD 180 2.081 -4.471 1.504 1.00 20.00 HETATM 41 C54 BCD 180 2.724 -2.946 3.238 1.00 20.00 HETATM 42 O54 BCD 180 3.789 -2.320 3.928 1.00 20.00 HETATM 43 C64 BCD 180 1.760 -3.465 4.363 1.00 20.00 HETATM 44 O64 BCD 180 1.472 -2.354 5.200 1.00 20.00 HETATM 45 C15 BCD 180 1.443 -5.730 1.674 1.00 20.00 HETATM 46 C25 BCD 180 1.155 -6.310 0.305 1.00 20.00 HETATM 47 O25 BCD 180 2.316 -6.297 -0.546 1.00 20.00 HETATM 48 C35 BCD 180 0.062 -5.488 -0.385 1.00 20.00 HETATM 49 O35 BCD 180 -0.309 -6.102 -1.631 1.00 20.00 HETATM 50 C45 BCD 180 -1.148 -5.406 0.509 1.00 20.00 HETATM 51 O45 BCD 180 -2.068 -4.506 -0.157 1.00 20.00 HETATM 52 C55 BCD 180 -0.803 -4.814 1.898 1.00 20.00 HETATM 53 O55 BCD 180 0.291 -5.571 2.462 1.00 20.00 HETATM 54 C65 BCD 180 -1.956 -4.953 2.815 1.00 20.00 HETATM 55 O65 BCD 180 -1.844 -4.161 3.971 1.00 20.00 HETATM 56 C16 BCD 180 -3.442 -4.906 -0.253 1.00 20.00 HETATM 57 C26 BCD 180 -3.851 -4.763 -1.672 1.00 20.00 HETATM 58 O26 BCD 180 -2.771 -5.259 -2.483 1.00 20.00 HETATM 59 C36 BCD 180 -4.097 -3.312 -2.088 1.00 20.00 HETATM 60 O36 BCD 180 -4.936 -3.353 -3.292 1.00 20.00 HETATM 61 C46 BCD 180 -4.746 -2.478 -1.084 1.00 20.00 HETATM 62 O46 BCD 180 -4.480 -1.097 -1.505 1.00 20.00 HETATM 63 C56 BCD 180 -4.167 -2.668 0.310 1.00 20.00 HETATM 64 O56 BCD 180 -4.230 -4.082 0.600 1.00 20.00 HETATM 65 C66 BCD 180 -4.910 -1.973 1.455 1.00 20.00 HETATM 66 O66 BCD 180 -5.517 -2.856 2.156 1.00 20.00 HETATM 67 C17 BCD 180 -5.599 -0.446 -2.126 1.00 20.00 HETATM 68 C27 BCD 180 -5.161 0.063 -3.479 1.00 20.00 HETATM 69 O27 BCD 180 -4.414 -0.971 -4.164 1.00 20.00 HETATM 70 C37 BCD 180 -4.270 1.294 -3.379 1.00 20.00 HETATM 71 O37 BCD 180 -4.187 1.908 -4.682 1.00 20.00 HETATM 72 C47 BCD 180 -4.808 2.340 -2.388 1.00 20.00 HETATM 73 O47 BCD 180 -3.692 3.241 -2.220 1.00 20.00 HETATM 74 C57 BCD 180 -5.048 1.639 -1.046 1.00 20.00 HETATM 75 O57 BCD 180 -6.026 0.572 -1.269 1.00 20.00 HETATM 76 C67 BCD 180 -5.683 2.573 -0.016 1.00 20.00 HETATM 77 O67 BCD 180 -4.985 2.346 1.209 1.00 20.00 REMARK BCD ENDHET