Avidin

spinqualitylabelsall models The avidin tetramer complex with biotin (PDB code 2avi) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Avidin (Av) is a protein found in egg white which binds biotin (vitamin B7) with high affinity. This property makes it a powerful tool in various protein pull-down assays. Similar proteins are: Streptavidin (StrAv) from the bacterium Streptomyces avidinii Rhizavidin (RhiAv) from Rhizobium etli Xenavidin from frog Tamavidin from fungi Bradavidin from Bradyrhizobium japonicum Hoefavidin from Hoeflea phototrophica Shwanavidin from Shewanella dentrifica AVR2 and AVR4 are avidin-related proteins. Avidin is one of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground. Avidin is a tetrameric protein what in different words means that if we could, we would see a protein with four regions that look identical one to the other. However, to isolate the four regions as a whole in order to show the protein three dimensional structure has been quite diffucult so far and we just can see the three dimensional structure for two of those four units. The binding affinity of biotin for the avidin receptors is very hight or in other words, the strength of the interations between the biotin and the avidin receptors is so strong that washing the biotin-avidin complex is not enough to remove the ligand from its pocket. This is not even possible by adding more biotin molecules to the system avidin-biotin. Once a biotin has bound a pocket in the avidin, it is almost imposible to remove it in a biologica system! Each monomer is an eight-stranded antiparallel beta-barrel. Binding of biotin involves a highly stabilized network of polar and hydrophobic interactions. The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin may account for its higher affinity constant. Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer. These sugars appear along with the biotin but outside of the biotin binding pockets. See also: Molecular Playground/Streptavidin Streptavidin Binding Site. About this Structure 2avi is a 2 chains structure of sequences from Gallus gallus. Full crystallographic information is available from OCA.

3D structures of Avidin

Updated on 12-January-2016

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• Avidin
  • CBI Molecules, Molecular Playground/Streptavidin, Streptavidin Binding Site, 2avi, 1rav, 1ave – cAv – chicken
    
  • 2a5b, 2a5c, 2a8g – cAv+deoxyribose
    
  • 1nqn, 2cam, 4bcs – cAv (mutant)
    
  • 1ldo, 1ldq, 1lel, 1ij8, 1avd, 2avi, 3vgw, 3vhh, 3vhi, 3vhm, 4i60, 4jhq – cAV + biotin derivative
    
  • 3szh, 3szi – SdAV – Shewanella denitrificans
    
  • 3t2x – SdAV (mutant)
    
  • 3szj – SdAV + biotin
    
  • 3t2w – SdAV (mutant) + biotin
• Streptavidin
  • 2bc3, 2iza, 2izb, 2izc, 2izd, 2ize, 2rta, 2rtb, 2rtc, 3ry1, 4gd9. 4gda, 4gjs - StrAv - Streptomyces avidinii
    
  • 3mm0, 3pk2, 3rds, 3rdx, 3re5, 3re6, 4gjv - StrAv (mutant)
    
  • 1swa, 1swb, 1swc, 1ry1 - StrAv core
    
  • 1swh, 1swj, 1swl, 1swo, 1swq, 1sws, 2y3e, 3t6l - StrAv core (mutant)
    
  • 4jnj – StrAv/rhizavidin
    
  • 4jo6 – StrAv + SBP-TAG
    
• Streptavidin binary complexes
  • 1rxh – StrAv (mutant)+ biotinyl p-nitroaniline
    
  • 1rxj, 1rxk, 1nqm, 1kff, 1kl4, 1luq, 1mm9, 1moy, 1n4j, 1n7y, 1n9y, 1nbx, 1swf, 1swu, 1kl3, 1kl5 - StrAv (mutant) + strep-tag II peptide
    
  • 1rst, 1rsu - StrAv + strep-tag II peptide
    
  • 1df8, 1mep, 1n43, 1n9m, 1ndj, 1swg, 3rdm, 3rdo, 4ekv - StrAv (mutant)+biotin
    
  • 1nc9, 3rdq, 4dne - StrAv (mutant)+biotin derivative
    
  • 2izl, 2rtl, 2rtm, 2rtn, 2rto, 2rtp, 2rtq, 2rtr - StrAv +iminobiotin
    
  • 1mk5, 1swd, 1swe, 2f01, 2gh7, 3ry2 - StrAv core+biotin
    
  • 1swk, 1swn, 1swp, 1swr, 1swt, 3mg5, 2y3f, 3t6f - StrAv core (mutant) + biotin
    
  • 1stp, 2izf, 2izg, 2izh, 2izi, 2izj, 2rtd, 2rte, 2rtf, 2rtg - StrAv +biotin
    
  • 3rdu - StrAv (mutant) + PEG
    
  • 1hqq, 1hxl – StrAv + MP-2 (mutant)
    
  • 1hy2 - StrAv + MP-1
    
  • 1hxz - StrAv + MP-2
    
  • 1pts, 1sld, 1sle, 1slg, 1str, 1sts, 1vwa, 1vwb, 1vwc, 1vwd, 1vwe, 1vwf, 1vwg, 1vwh, 1vwi, 1vwj, 1vwk, 1vwl, 1vwm, 1vwn, 1vwo, 1vwp, 1vwq, 1vwr, 2g5l - StrAv + peptide
    
  • 1slf - StrAv + SO4
    
  • 1sre, 1srf, 1srg, 1srh, 1sri, 1srj - StrAv + benzoic acid ligands
    
  • 1lcv, 1lcw, 1lcz, 1i9h – StrAv+biotin derivative
    
  • 2izk, 2rth, 2rti, 2rtj, 2rtk – StrAV+glycouril
    
  • 2qcb, 2wpu – StrAv+Ru ligand
• Rhizavidin
  • 3ew1 – RhiAv – Rhizobium etli
    
  • 3ew2 – RhiAV+biotin
    
• Xenavidin
  • 2uz2, 2uyw – XenAv – frog
    
• Tamavidin
  • 2zsc – TanAv – Tamogitake mushroom
• Bradavidin
  • 4ggr, 4ggt – BjAv – Bradyrhizobium japonicum
    
  • 4ggz – BjAv + biotin
    
• Hoefavidin
  • 4z6j – HpAv – Hoeflea phototrophica
    
  • 4z27 – HpAv short
    
  • 4z28 – HpAv short + biotin
    
  • 4z2p, 4z2v, 4z2o – HpAv short + peptide
    
• Shwanavidin
  • 3szi, 3szh – SdAv – Shewanella dentrifica
    
  • 3t2x – SdAv (mutant)
    
  • 3szj – SdAv + biotin
    
  • 3t2w – SdAv (mutant) + biotin
    
• Avidin-related protein AVR2
  • 1wbi – cAVR2
    
• Avidin-related protein AVR4
  • 2fhl – cAVR4+biotinyl p-nitroaniline
    
  • 2of9, 2ofa, 1y53, 3mm0 - cAVR4 (mutant)
    
  • 2fhn, 2of8, 2ofb - cAVR4 (mutant)+biotinyl p-nitroaniline
    
  • 1y52, 1y55 - cAVR4 (mutant)+biotin
    
  • 2mf6 - cAVR4/Av (mutant)+biotin – NMR
    

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