1avd: Difference between revisions
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|PDB= 1avd |SIZE=350|CAPTION= <scene name='initialview01'>1avd</scene>, resolution 2.7Å | |PDB= 1avd |SIZE=350|CAPTION= <scene name='initialview01'>1avd</scene>, resolution 2.7Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=BTN:BIOTIN'>BTN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1avd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1avd OCA], [http://www.ebi.ac.uk/pdbsum/1avd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1avd RCSB]</span> | |||
}} | }} | ||
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[[Category: Malcovati, M.]] | [[Category: Malcovati, M.]] | ||
[[Category: Pugliese, L.]] | [[Category: Pugliese, L.]] | ||
[[Category: biotin-binding protein]] | [[Category: biotin-binding protein]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:48:17 2008'' | ||
Revision as of 18:48, 30 March 2008
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| , resolution 2.7Å | |||||||
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| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION
OverviewOverview
The three-dimensional structure of hen egg-white avidin, crystallized in a tetragonal crystal form, has been solved at 2.7 A resolution by molecular replacement methods. After refinement the crystallographic R-factor is 16.8%, for the 7255 reflections in the 10.0 to 2.7 A resolution range. The asymmetric unit contains two avidin polypeptide chains (M(r) 2 x 15,600), which build up the functional tetramer through a crystallographic 2-fold axis parallel to the c unit cell direction. The avidin tetramer has almost exact 222 molecular symmetry; the three possible dimers display quite distinct packing interfaces. Each protomer is organized in an eight-stranded antiparallel orthogonal beta-barrel, with extended loop regions. The avidin binding site within each promoter is located in a deep pocket, at the center of the barrel, displaying both hydrophobic and polar residues for recognition of the tightly bound vitamin. Two Trp residues, Trp70 and Trp97, and Phe79 are in close contact with biotin. Moreover, the binding pocket is partly closed in its outer rim by residue Trp110 of a neighboring subunit. Once bound, biotin is almost completely buried in the protein core, with the exception of the valeryl side-chain carboxylate group which is exposed to solvent, hydrogen bonds to residues Ala39, Thr40 and Ser75, and triggers the formation of a network of hydrogen bonded water molecules. Modeling of synthetic biotin analogues allows us to rationalize functional data available for the binding of these compounds, and to analyze them in terms of biotin recognition mechanism. Hen egg-white avidin shows clear structural homology to streptavidin, from Streptomyces avidinii, but significant deviations can be observed in some regions.
About this StructureAbout this Structure
1AVD is a Single protein structure of sequence from Gallus gallus. Full crystallographic information is available from OCA.
ReferenceReference
Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution., Pugliese L, Coda A, Malcovati M, Bolognesi M, J Mol Biol. 1993 Jun 5;231(3):698-710. PMID:8515446
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