6H3H

Fab fragment of antibody against fullerene C60


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report



Literature

Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding.

Osipov, E.M.Hendrickson, O.D.Tikhonova, T.V.Zherdev, A.V.Solopova, O.N.Sveshnikov, P.G.Dzantiev, B.B.Popov, V.O.

(2019) Acta Naturae 11: 58-65

  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the anti-C 60 fullerene antibody Fab fragment (FabC 60 ) was solved by X-ray crystallography. The computer-aided docking of C 60 into the antigen-binding pocket of FabC 60 showed that binding of C 60 to FabC 60 is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C 60 ...

    The structure of the anti-C 60 fullerene antibody Fab fragment (FabC 60 ) was solved by X-ray crystallography. The computer-aided docking of C 60 into the antigen-binding pocket of FabC 60 showed that binding of C 60 to FabC 60 is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C 60 . A fragment of the mobile CDR H3 loop located on the surface of FabC 60 interferes with C 60 binding in the antigen-binding site, thereby resulting in low antibody affinity for C 60 . The structure of apo-FabC 60 has been deposited with pdbid 6H3H.


    Organizational Affiliation

    Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-fullerene antibody Fab fragment Heavy chainA, C222Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-fullerene antibody Fab fragment Light chainB, D215Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.33α = 90
b = 138.18β = 91.85
c = 83.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-24-00172

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release