|
|
| (11 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1dvl.gif|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END== |
| - | |PDB= 1dvl |SIZE=350|CAPTION= <scene name='initialview01'>1dvl</scene>, resolution 2.4Å
| + | <StructureSection load='1dvl' size='340' side='right'caption='[[1dvl]], [[Resolution|resolution]] 2.40Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DI:2'-DEOXYINOSINE-5'-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=NT:NETROPSIN'>NT</scene>
| + | <table><tr><td colspan='2'>[[1dvl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVL FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvl OCA], [https://pdbe.org/1dvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvl RCSB], [https://www.ebi.ac.uk/pdbsum/1dvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvl ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvl OCA], [http://www.ebi.ac.uk/pdbsum/1dvl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dvl RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END'''
| + | [[Category: Mitra SN]] |
| - | | + | [[Category: Shi K]] |
| - | | + | [[Category: Sundaralingam M]] |
| - | ==Overview==
| + | |
| - | The crystal structure of the 1:1 complex of netropsin and the B-DNA decamer d(CCIICICCII)(2) has been elucidated and refined to an R factor of 19.6% and an R(free) of 24.7% using 1790 reflections in the resolution range 8-2.4 A. The complex crystallizes in space group C2, with unit-cell parameters a = 62.40, b = 24.47, c = 36.31 A, beta = 110.09 degrees and one molecule of netropsin in the asymmetric unit; the rest of the minor groove is filled with six water molecules. The structure was solved by the molecular-replacement method using the DNA model d(CCCCCIIIII)(2) from the 2:1 netropsin complex by removing both bound netropsins (Chen et al., 1998). Surprisingly, only one netropsin molecule is found to bind to the present decamer, covering residues 2-6 at the upper stream of the duplex. The positively charged guanidinium head is hydrogen bonded through N1H(2) to the O(2) of cytosine 2 and through N10H(2) to N(3) of inosine 6. The three amide N-H groups of the peptides face the minor groove and form three sets of bifurcated hydrogen bonds with the base atoms. The central part of the drug (C3-N8) is nearly conjugated. The preference of the cytosine carbonyl O2 atoms over the inosine N3 atoms in hydrogen bonding is seen. The drug-bound region has more uniform twists, roll angles, propeller twists and minor-groove widths compared with the water-bound region.
| + | |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1DVL is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVL OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin., Shi K, Mitra SN, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):601-6. Epub 2002, Mar 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11914483 11914483]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Mitra, S N.]] | + | |
| - | [[Category: Shi, K.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: drug binding]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:49:34 2008''
| + | |
