1dwl
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1dwl.gif|left|200px]]< | + | [[Image:1dwl.gif|left|200px]] |
| - | + | ||
| - | '''THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR AND DOCKING SIMULATION''' | + | {{Structure |
| + | |PDB= 1dwl |SIZE=350|CAPTION= <scene name='initialview01'>1dwl</scene> | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene> and <scene name='pdbligand=HEC:HEME C'>HEC</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= FDXI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=876 Desulfovibrio desulfuricans]) | ||
| + | }} | ||
| + | |||
| + | '''THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR AND DOCKING SIMULATION''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1DWL is a [ | + | 1DWL is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans] and [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DWL OCA]. |
==Reference== | ==Reference== | ||
| - | Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex., Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F, Biochemistry. 2000 Mar 14;39(10):2530-7. PMID:[http:// | + | Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex., Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F, Biochemistry. 2000 Mar 14;39(10):2530-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10704202 10704202] |
[[Category: Desulfovibrio desulfuricans]] | [[Category: Desulfovibrio desulfuricans]] | ||
[[Category: Desulfovibrio vulgaris]] | [[Category: Desulfovibrio vulgaris]] | ||
| Line 26: | Line 35: | ||
[[Category: model]] | [[Category: model]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:45:35 2008'' |
Revision as of 08:45, 20 March 2008
| |||||||
| Ligands: | and | ||||||
| Gene: | FDXI (Desulfovibrio desulfuricans) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR AND DOCKING SIMULATION
Overview
The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. The cytochrome c553-ferredoxin complex is used as a model of numerous electron-transfer complexes. The 15N-labeling of both molecules has been obtained, and the mapping of the interacting site on each partner, respectively, has been done using HSQC experiments. 1H and 15N chemical shift analysis defines the area of both molecules involved in the recognition interface. Models of the complex were generated by an ab initio docking software, the BiGGER program (bimolecular complex generation with global evaluation and ranking). This program generates a population of protein-protein docked geometries ranked by a scoring function, combining relevant stabilization parameters such as geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We have implemented a new module that includes experimental input (here, NMR mapping of the interacting site) as a filter to select the accurate models. Final structures were energy minimized using the X-PLOR software and then analyzed. The best solution has an interface area (1037.4 A2) falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.
About this Structure
1DWL is a Protein complex structure of sequences from Desulfovibrio desulfuricans and Desulfovibrio vulgaris. Full crystallographic information is available from OCA.
Reference
Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex., Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F, Biochemistry. 2000 Mar 14;39(10):2530-7. PMID:10704202
Page seeded by OCA on Thu Mar 20 10:45:35 2008
